Index

A B C D E F G H I K L M N O P Q R S T U V W X Y Z

A

abortAcquisition() - Method in interface org.micromanager.acquisition.AcquisitionManager: Abort any ongoing acquisition as soon as possible, without user dialog.
AbstractDataViewer - Class in org.micromanager.display: Abstract implementation of the DataViewer interface.
AbstractDataViewer(DisplaySettings) - Constructor for class org.micromanager.display.AbstractDataViewer: Construct the abstract viewer implementation.
AbstractInspectorPanelController - Class in org.micromanager.display.inspector: A panel containing a section of the inspector window.
AbstractInspectorPanelController() - Constructor for class org.micromanager.display.inspector.AbstractInspectorPanelController
AbstractOverlay - Class in org.micromanager.display.overlay: Abstract implementation of Overlay.
AbstractOverlay() - Constructor for class org.micromanager.display.overlay.AbstractOverlay
acqOrderMode() - Method in class org.micromanager.acquisition.SequenceSettings: Order of the various axes during acquisition as defined in AcqOrderMode.
acqOrderMode(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder: Sets acquisition order of axes.
AcquisitionEndedEvent - Interface in org.micromanager.acquisition: This event signifies that an acquisition has been ended.
AcquisitionManager - Interface in org.micromanager.acquisition: This interface provides access to methods related to the acquisition engine for performing experiments.
acquisitions() - Method in interface org.micromanager.Studio: Provide access to the AcquisitionManager, for running data acquisition using the Micro-Manager acquisition engine.
AcquisitionSequenceStartedEvent - Interface in org.micromanager.acquisition: This variant of the AcquisitionStartedEvent is used for acquisitions that can be described by a SequenceSettings, it provides access to those SequenceSettings.
AcquisitionSettingsChangedEvent - Interface in org.micromanager.acquisition: The default implementation of this event posts on the Studio event bus, so subscribe to this event using EventManager.
AcquisitionStartedEvent - Interface in org.micromanager.acquisition: This class signals that an acquisition is starting, and provides access to the Datastore that images from the acquisition will be put into.
activate() - Method in class org.micromanager.quickaccess.SimpleButtonPlugin: This method will be called when the button is clicked.
add(StagePosition) - Method in class org.micromanager.MultiStagePosition: Add one stage position point.
addAndConfigureProcessor(ProcessorPlugin) - Method in interface org.micromanager.data.DataManager: Add a new instance of the given ProcessorPlugin to the current application image processing pipeline.
addChangeListener(ChangeListener) - Method in class org.micromanager.PositionList: Adds a changeListener to this PositionList.
addConfiguredProcessor(ProcessorConfigurator, ProcessorPlugin) - Method in interface org.micromanager.data.DataManager: Add the provide ProcessorConfigurator onto the end of the application image processing pipeline.
addImage(Image) - Method in interface org.micromanager.Album: Add the specified Image to the Album's datastore.
addImages(Collection<Image>) - Method in interface org.micromanager.Album: Add the specified Images to the Album's datastore.
addInspectorPanelListener(InspectorPanelListener) - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
addInspectorPanelListener(InspectorPanelListener) - Method in interface org.micromanager.display.inspector.InspectorPanelController
addListener(DataViewerListener, int) - Method in interface org.micromanager.display.DataViewer: Listeners will be notified of important events of the DataViewer.
addOverlay(Overlay) - Method in interface org.micromanager.display.DisplayWindow: Add a graphical overlay.
addOverlayListener(OverlayListener) - Method in class org.micromanager.display.overlay.AbstractOverlay: Add a listener.
addOverlayListener(OverlayListener) - Method in interface org.micromanager.display.overlay.Overlay: Add a listener.
addPosition(MultiStagePosition) - Method in class org.micromanager.PositionList: Adds a new position to the list.
addPosition(int, MultiStagePosition) - Method in class org.micromanager.PositionList: Insert a position into the list.
addViewer(DataViewer) - Method in interface org.micromanager.display.DisplayManager: Register a DataViewer with the Display Manager.
adjustZoom(double) - Method in interface org.micromanager.display.DisplayWindow: Multiply the current zoom ratio of the image canvas by the provided factor.
Album - Interface in org.micromanager: Interface for interacting with the Album, an implicit Datastore that Micro-Manager uses as a "scratch pad" for image data.
album() - Method in interface org.micromanager.Studio: Provides access to and control of the contents of the Album, the implicit, temporary image storage datastore.
Alert - Interface in org.micromanager.alerts: An Alert is a temporary, undecorated message that is displayed to the user in the Messages window.
AlertManager - Interface in org.micromanager.alerts: The AlertManager allows you to show non-intrusive messages to the user, which will be displayed in a special window, the Messages window.
alerts() - Method in interface org.micromanager.Studio: Provide access to the AlertManager, for creating low-profile, non- interrupting alerts in the user interface.
animationFPS(Double) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
Annotation - Interface in org.micromanager.data: A Annotation is a container for mutable information that is associated with a Datastore.
app() - Method in interface org.micromanager.Studio: Provides access to the application API for controlling and updating the GUI.
Application - Interface in org.micromanager: Provides access to and control of various aspects of the user interface, allowing code to directly update and control the GUI.
ApplicationSkin - Interface in org.micromanager: Provides access to methods dealing with the "skin" or "look and feel" of the user interface.
ApplicationSkin.SkinMode - Enum in org.micromanager: Available skins used by the application.
ApplicationSkinEvent - Interface in org.micromanager.events: This event is posted when the ApplicationSkin is set via ApplicationSkin.setSkin(org.micromanager.ApplicationSkin.SkinMode).
applySettings() - Method in interface org.micromanager.AutofocusPlugin: Pushes setting to the hardware or software autofocus.
attachDataViewer(DataViewer) - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController: Attach to a data viewer.
attachDataViewer(DataViewer) - Method in interface org.micromanager.display.inspector.InspectorPanelController
attachRunnable(int, int, int, int, Runnable) - Method in interface org.micromanager.acquisition.AcquisitionManager: Attach a runnable to the acquisition engine.
AutofocusManager - Interface in org.micromanager: This entity provides access to methods for controlling autofocus of the microscope.
AutofocusPlugin - Interface in org.micromanager: This interface is used for a java-based autofocus plugin.
AutofocusPluginShouldInitializeEvent - Class in org.micromanager.events: Deprecated.
use
AutofocusPluginShouldInitializeEvent() - Constructor for class org.micromanager.events.AutofocusPluginShouldInitializeEvent: Deprecated.
autoscaleIgnoredPercentile(double) - Method in interface org.micromanager.display.DisplaySettings.Builder
autoscaleIgnoredQuantile(double) - Method in interface org.micromanager.display.DisplaySettings.Builder
autoscaleIgnoringZeros(boolean) - Method in interface org.micromanager.display.DisplaySettings.Builder
AutoShutterEvent - Interface in org.micromanager.events: This event is posted when autoshutter is enabled or disabled.
autostretch(boolean) - Method in interface org.micromanager.display.DisplaySettings.Builder: Whether to continuously apply autoscale.
autostretch() - Method in interface org.micromanager.display.DisplayWindow: Performs a one-shot autoscaling of intensities.
axisOrder(String...) - Method in interface org.micromanager.data.SummaryMetadata.Builder
axisOrder(Iterable<String>) - Method in interface org.micromanager.data.SummaryMetadata.Builder
axisOrder(String...) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.

B

binning(Integer) - Method in interface org.micromanager.data.Metadata.Builder
binning(Integer) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
bitDepth(Integer) - Method in interface org.micromanager.data.Metadata.Builder
bitDepth(Integer) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
build() - Method in class org.micromanager.acquisition.ChannelSpec.Builder
build() - Method in class org.micromanager.acquisition.SequenceSettings.Builder: Constructs SequenceSettings.
build() - Method in interface org.micromanager.data.Coords.Builder
build() - Method in interface org.micromanager.data.Coords.CoordsBuilder
build() - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.

Construct a Metadata from the MetadataBuilder.
build() - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
build() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
build() - Method in interface org.micromanager.display.ComponentDisplaySettings.Builder
build() - Method in interface org.micromanager.display.DisplaySettings.Builder
build() - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
build() - Method in interface org.micromanager.PropertyMap.Builder
build() - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
Builder() - Constructor for class org.micromanager.acquisition.ChannelSpec.Builder
Builder() - Constructor for class org.micromanager.acquisition.SequenceSettings.Builder
Builder(SequenceSettings) - Constructor for class org.micromanager.acquisition.SequenceSettings.Builder: Construct a Builder using the given SequenceSettings (copy builder).
builder() - Static method in class org.micromanager.data.Coordinates
builder() - Static method in class org.micromanager.PropertyMaps: Returns a builder object for creating PropertyMap instances.

C

c(int) - Method in interface org.micromanager.data.Coords.Builder: Shorthand for channel.
C - Static variable in interface org.micromanager.data.Coords: Axis label for the channel axis (short form).
camera(String) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
camera - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
camera() - Method in class org.micromanager.acquisition.ChannelSpec
camera(String) - Method in interface org.micromanager.data.Metadata.Builder
camera(String) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
cameraTimeout(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
cameraTimeout - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and cameraTimeout() instead
cameraTimeout() - Method in class org.micromanager.acquisition.SequenceSettings: Minimum camera timeout, in ms, for sequence acquisitions (actual timeout depends on exposure time and other factors).
cancelShutdown() - Method in interface org.micromanager.events.ShutdownCommencingEvent: Cancel shutdown.
canCloseViewer(DataViewer) - Method in class org.micromanager.display.DataViewerListener: Whether or not the DataViewer can be closed.
CELL_HEIGHT - Static variable in class org.micromanager.quickaccess.QuickAccessPlugin: The height of a single cell in the Quick-Access Window.
CELL_WIDTH - Static variable in class org.micromanager.quickaccess.QuickAccessPlugin: The width of a single cell in the Quick-Access Window.
channel(int) - Method in interface org.micromanager.data.Coords.Builder: Set the channel index.
CHANNEL - Static variable in interface org.micromanager.data.Coords: Axis label for the channel axis.
channel(int) - Method in interface org.micromanager.data.Coords.CoordsBuilder
channel(int) - Method in interface org.micromanager.display.DisplaySettings.Builder: Increases the number of ChannelDisplaySettings in this Builder to the given number.
channel(int, ChannelDisplaySettings) - Method in interface org.micromanager.display.DisplaySettings.Builder: Sets the ChannelDisplaySettings for the given channel.
channelColorMode(DisplaySettings.ColorMode) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
channelColors(Color[]) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
channelContrastSettings(DisplaySettings.ContrastSettings[]) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
ChannelDisplaySettings - Interface in org.micromanager.display: Stores the display settings for individual channels Coords of image to be displayed.
ChannelDisplaySettings.Builder - Interface in org.micromanager.display: Builder for ChannelDisplaySettings.
channelDisplaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager: Generates a blank channelDisplaySettings Builder with all null values.
ChannelExposureEvent - Interface in org.micromanager.events: This class signals when the exposure time for one of the channels of the current channel group has been changed.
channelGroup(String) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
channelGroup - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
channelGroup() - Method in class org.micromanager.acquisition.ChannelSpec
channelGroup(String) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
channelGroup - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and channelGroup() instead
channelGroup() - Method in class org.micromanager.acquisition.SequenceSettings: Configuration group used to define channels used in the acquisition.
channelGroup(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
channelGroup(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
ChannelGroupChangedEvent - Interface in org.micromanager.events: Event signaling that the "Channel Group" changed.
channelNames(String...) - Method in interface org.micromanager.data.SummaryMetadata.Builder
channelNames(Iterable<String>) - Method in interface org.micromanager.data.SummaryMetadata.Builder
channelNames(String...) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
channels(ArrayList<ChannelSpec>) - Method in class org.micromanager.acquisition.SequenceSettings.Builder: Sets the ChannelSpecs to be used in this builder.
channels - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and channels() instead
channels() - Method in class org.micromanager.acquisition.SequenceSettings: List with channel definitions to be used in the acquisition.
channels(Iterable<ChannelDisplaySettings>) - Method in interface org.micromanager.display.DisplaySettings.Builder: Replaces ChannelDisplaySettings with those given.
ChannelSpec - Class in org.micromanager.acquisition: A ChannelSpec is a description of how a specific channel will be used in an MDA (multi-dimensional acquisition).
ChannelSpec() - Constructor for class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder.build() instead for a default ChannelSpec
ChannelSpec.Builder - Class in org.micromanager.acquisition: ChannelSpec Builder.
channelSpecBuilder() - Method in interface org.micromanager.acquisition.AcquisitionManager: Provides and empty ChannelSpec Builder.
cleanup(ProcessorContext) - Method in interface org.micromanager.data.Processor: Clean up when processing is finished.
cleanup() - Method in interface org.micromanager.data.ProcessorConfigurator: Remove any GUI resources currently in use.
clear() - Method in interface org.micromanager.PropertyMap.Builder
clear() - Method in interface org.micromanager.propertymap.MutablePropertyMapView
clearAllPositions() - Method in class org.micromanager.PositionList: Empties the list.
clearExceptions() - Method in interface org.micromanager.data.Pipeline: Clear the list of exceptions that the pipeline has encountered, allowing insertImage() to be called again.
clearMessageWindow() - Method in interface org.micromanager.ScriptController: Clears scripting console output window.
clearPipeline() - Method in interface org.micromanager.data.DataManager: Clear the current application pipeline, so that no on-the-fly image processing is performed.
clearRunnables() - Method in interface org.micromanager.acquisition.AcquisitionManager: Remove runnables from the acquisition engine.
clearSettingsForAllClasses() - Method in interface org.micromanager.UserProfile: Reset this user profile, deleting all settings.
close() - Method in interface org.micromanager.data.DataProvider
close() - Method in interface org.micromanager.data.Storage: Release any resources used by the Storage, for example open file descriptors.
close() - Method in interface org.micromanager.display.DisplayWindow: Close this display window unconditionally.
closeAllDisplayWindows(boolean) - Method in interface org.micromanager.display.DisplayManager: Close all open image windows.
closeDisplaysFor(DataProvider) - Method in interface org.micromanager.display.DisplayManager: Given a DataProvider, close any open DisplayWindows for that DataProvider.
color(Color) - Method in class org.micromanager.acquisition.ChannelSpec.Builder: Deprecated.
use ChannelDisplaySettings.color() instead
color - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
color() - Method in class org.micromanager.acquisition.ChannelSpec
color(Color) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorBlue() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorColorBlindFriendly(int) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorCyan() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorGreen() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorMagenta() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorMode(DisplaySettings.ColorMode) - Method in interface org.micromanager.display.DisplaySettings.Builder: Color mode or lookup table for displaying the image.
colorModeComposite() - Method in interface org.micromanager.display.DisplaySettings.Builder
colorModeGrayscale() - Method in interface org.micromanager.display.DisplaySettings.Builder
colorModeHighlightSaturated() - Method in interface org.micromanager.display.DisplaySettings.Builder
colorModeSingleColor() - Method in interface org.micromanager.display.DisplaySettings.Builder
colorRed() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorWhite() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
colorYellow() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
comment(String) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
comment - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and comment() instead
comment() - Method in class org.micromanager.acquisition.SequenceSettings: Text comment to be attached to the acquired data.
compareAndSetDisplayPosition(Coords, Coords, boolean) - Method in class org.micromanager.display.AbstractDataViewer: Implements compareAndSetDisplayPosition.
compareAndSetDisplayPosition(Coords, Coords) - Method in class org.micromanager.display.AbstractDataViewer
compareAndSetDisplayPosition(Coords, Coords, boolean) - Method in interface org.micromanager.display.DataViewer: Set the display position only if the current position is the expected one.
compareAndSetDisplayPosition(Coords, Coords) - Method in interface org.micromanager.display.DataViewer: Set the display position only if the current position is the expected one.
compareAndSetDisplaySettings(DisplaySettings, DisplaySettings) - Method in class org.micromanager.display.AbstractDataViewer: Implements compareAndSetDisplaySettings.
compareAndSetDisplaySettings(DisplaySettings, DisplaySettings) - Method in interface org.micromanager.display.DataViewer: Set the display settings only if the current settings match the expected one.
compat() - Method in interface org.micromanager.Studio: Provides access to the compatibility layer that exposes some old 1.4 API methods.
CompatibilityInterface - Interface in org.micromanager: Legacy interface that implements some methods from the old 1.4 API.
component(int) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
component(int, ComponentDisplaySettings) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
ComponentDisplaySettings - Interface in org.micromanager.display: Certain cameras (such as RGB cameras) can produce images where each pixel has multiple components.
ComponentDisplaySettings.Builder - Interface in org.micromanager.display: Interface for ComponentDisplaySettings Builder.
componentDisplaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager: Generates a blank componentSettings Builder with all null values.
computerName(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
computerName(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
computeScore(ImageProcessor) - Method in interface org.micromanager.AutofocusPlugin: Computes a focus score for the given image.
config(String) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
config - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
config() - Method in class org.micromanager.acquisition.ChannelSpec
ConfigGroupChangedEvent - Interface in org.micromanager.events: Event signaling that the "active" preset in a config group changed.
configureControl(Frame) - Method in class org.micromanager.quickaccess.WidgetPlugin: Generate configuration information that can be used to configure a control generated by this plugin.
containsAffineTransform(String) - Method in interface org.micromanager.PropertyMap
containsAffineTransform(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsAffineTransformList(String) - Method in interface org.micromanager.PropertyMap
containsAffineTransformList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsAll(Collection<?>) - Method in interface org.micromanager.PropertyMap
containsAll(Collection<?>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView: Return whether all of the given keys are present in this view.
containsBoolean(String) - Method in interface org.micromanager.PropertyMap
containsBoolean(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsBooleanList(String) - Method in interface org.micromanager.PropertyMap
containsBooleanList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsByte(String) - Method in interface org.micromanager.PropertyMap
containsByte(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsByteList(String) - Method in interface org.micromanager.PropertyMap
containsByteList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsColor(String) - Method in interface org.micromanager.PropertyMap
containsColor(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsColorList(String) - Method in interface org.micromanager.PropertyMap
containsColorList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsDimension(String) - Method in interface org.micromanager.PropertyMap
containsDimension(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsDimensionList(String) - Method in interface org.micromanager.PropertyMap
containsDimensionList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsDouble(String) - Method in interface org.micromanager.PropertyMap
containsDouble(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsDoubleList(String) - Method in interface org.micromanager.PropertyMap
containsDoubleList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsFloat(String) - Method in interface org.micromanager.PropertyMap
containsFloat(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsFloatList(String) - Method in interface org.micromanager.PropertyMap
containsFloatList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsInteger(String) - Method in interface org.micromanager.PropertyMap
containsInteger(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsIntegerList(String) - Method in interface org.micromanager.PropertyMap
containsIntegerList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsKey(String) - Method in interface org.micromanager.PropertyMap
containsKey(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView: Return whether a given key is present in this view.
containsLong(String) - Method in interface org.micromanager.PropertyMap
containsLong(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsLongList(String) - Method in interface org.micromanager.PropertyMap
containsLongList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsNumber(String) - Method in interface org.micromanager.PropertyMap
containsNumber(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsNumberList(String) - Method in interface org.micromanager.PropertyMap
containsNumberList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsPoint(String) - Method in interface org.micromanager.PropertyMap
containsPoint(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsPointList(String) - Method in interface org.micromanager.PropertyMap
containsPointList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsPropertyMap(String) - Method in interface org.micromanager.PropertyMap
containsPropertyMap(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsPropertyMapList(String) - Method in interface org.micromanager.PropertyMap
containsPropertyMapList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsRectangle(String) - Method in interface org.micromanager.PropertyMap
containsRectangle(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsRectangleList(String) - Method in interface org.micromanager.PropertyMap
containsRectangleList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsShort(String) - Method in interface org.micromanager.PropertyMap
containsShort(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsShortList(String) - Method in interface org.micromanager.PropertyMap
containsShortList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsString(String) - Method in interface org.micromanager.PropertyMap
containsString(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsStringForEnum(String, Class<E>) - Method in interface org.micromanager.PropertyMap
containsStringForEnum(String, Class<E>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsStringList(String) - Method in interface org.micromanager.PropertyMap
containsStringList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsStringListForEnumList(String, Class<E>) - Method in interface org.micromanager.PropertyMap
containsStringListForEnumList(String, Class<E>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsUUID(String) - Method in interface org.micromanager.PropertyMap
containsUUID(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
containsUUIDList(String) - Method in interface org.micromanager.PropertyMap
containsUUIDList(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
convertTaggedImage(TaggedImage) - Method in interface org.micromanager.data.DataManager: Given a TaggedImage input, output an Image based on the TaggedImage.
convertTaggedImage(TaggedImage, Coords, Metadata) - Method in interface org.micromanager.data.DataManager: Given a TaggedImage input, output an Image based on the TaggedImage, but with the Coords and/or Metadata optionally overridden.
Coordinates - Class in org.micromanager.data: Static helper functions to assist working with Coords.
Coords - Interface in org.micromanager.data: The multi-dimensional coordinate of a 2D image within a dataset.
Coords.Builder - Interface in org.micromanager.data: The real Builder for Coords.
Coords.CoordsBuilder - Interface in org.micromanager.data: Not sure why there is a Builder and CoordsBuilder.
coordsBuilder() - Method in interface org.micromanager.data.DataManager: Generate a "blank" CoordsBuilder for use in constructing new Coords instances.
copy() - Method in class org.micromanager.acquisition.SequenceSettings: Deprecated.
When used correctly, SequenceSettings are immutable. If you really need a copy, use copyBuilder().build();
copy() - Method in interface org.micromanager.data.Coords: Deprecated.
Use copyBuilder instead
copy() - Method in interface org.micromanager.data.Metadata: Deprecated.
Use the appropriate of the following: Metadata.copyBuilderPreservingUUID(), Metadata.copyBuilderWithNewUUID(), Metadata.copyBuilderRemovingUUID(). This method is equivalent to copyBuilderPreservingUUID.
copy() - Method in interface org.micromanager.data.SummaryMetadata: Deprecated.
- Use SummaryMetadata.Builder.copyBuilder instead
copy() - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
copy() - Method in interface org.micromanager.PropertyMap: Deprecated.
copyApplicationPipeline(Datastore, boolean) - Method in interface org.micromanager.data.DataManager: Create a copy of the current application Pipeline as configured in the "Data Processing Pipeline" window.
copyAtCoords(Coords) - Method in interface org.micromanager.data.Image: Generate a copy of this Image, except with different coordinates.
copyBuilder() - Method in class org.micromanager.acquisition.ChannelSpec
copyBuilder() - Method in class org.micromanager.acquisition.SequenceSettings
copyBuilder() - Method in interface org.micromanager.data.Coords: Provides a Builder pre-loaded with a copy of this Coords.
copyBuilder() - Method in interface org.micromanager.data.SummaryMetadata
copyBuilder() - Method in interface org.micromanager.display.ChannelDisplaySettings
copyBuilder() - Method in interface org.micromanager.display.ComponentDisplaySettings
copyBuilder() - Method in interface org.micromanager.display.DisplaySettings
copyBuilder() - Method in interface org.micromanager.PropertyMap
copyBuilderPreservingUUID() - Method in interface org.micromanager.data.Metadata: Return a builder with the same content, preserving the image UUID.
copyBuilderRemovingUUID() - Method in interface org.micromanager.data.Metadata: Return a builder with the same content but removing the image UUID.
copyBuilderWithChannelSettings(int, ChannelDisplaySettings) - Method in interface org.micromanager.display.DisplaySettings
copyBuilderWithComponentSettings(int, ComponentDisplaySettings) - Method in interface org.micromanager.display.ChannelDisplaySettings
copyBuilderWithComponentSettings(int, int, ComponentDisplaySettings) - Method in interface org.micromanager.display.DisplaySettings
copyBuilderWithNewUUID() - Method in interface org.micromanager.data.Metadata: Return a builder with the same content, assigning a new image UUID.
copyLivePipeline(Datastore, boolean) - Method in interface org.micromanager.data.DataManager: Create a copy of the current Live Pipeline as configured in the "Data Processing Pipeline" window.
copyRemovingAxes(String...) - Method in interface org.micromanager.data.Coords: Removes the axes provided as varargs from this Coord.
copyRetainingAxes(String...) - Method in interface org.micromanager.data.Coords: Name of this function is very unclear.
copyWith(Coords, Metadata) - Method in interface org.micromanager.data.Image: Generate a copy of this Image, except with different coordinates and metadata.
copyWithMetadata(Metadata) - Method in interface org.micromanager.data.Image: Generate a copy of this Image, except with different metadata.
core() - Method in interface org.micromanager.Studio: Provides access to the Core and its functionality.
create1D(String, double) - Static method in class org.micromanager.StagePosition: Creates a new StapePosition for a 1 axis drive.
create2D(String, double, double) - Static method in class org.micromanager.StagePosition: Creates a new StapePosition for a 2 axis drive.
createButton() - Method in class org.micromanager.quickaccess.ToggleButtonPlugin: Provide a JToggleButton that will behave as desired by the plugin.
createConfigurator(PropertyMap) - Method in interface org.micromanager.data.ProcessorPlugin: Generate any GUI needed to configure the plugin, using the provided settings to initialize the GUI.
createControl(PropertyMap) - Method in class org.micromanager.quickaccess.WidgetPlugin: Create the GUI components for this control.
createCoords(String) - Method in interface org.micromanager.data.DataManager: Deprecated.
use of Strings for Coords is discouraged
createDisplay(DataProvider) - Method in interface org.micromanager.display.DisplayManager: Create a new DisplayWindow for the specified DataProvider and return it.
createDisplay(DataProvider, DisplayWindowControlsFactory) - Method in interface org.micromanager.display.DisplayManager: Create a new DisplayWindow for the specified DataProvider and return it.
createExporter() - Method in interface org.micromanager.display.DisplayManager: Provide an ImagceExporter for generating image sequences.
createFactory(PropertyMap) - Method in interface org.micromanager.data.ProcessorPlugin: Generate a ProcessorFactory that can be used to generate Processor instances.
createFirstInspector() - Method in interface org.micromanager.display.DisplayManager: Deprecated.
createImage(Object, int, int, int, int, Coords, Metadata) - Method in interface org.micromanager.data.DataManager: Generate a new Image with the provided pixel data, rules for interpreting that pixel data, coordinates, and metadata.
createImage(ImageProcessor, Coords, Metadata) - Method in interface org.micromanager.data.ImageJConverter: Create a new Image based on the provided ImageProcessor and metadata.
createInspectorForDataViewer(DataViewer) - Method in interface org.micromanager.display.DisplayManager: Create a new Inspector window that shows information for the specified DataViewer, or for the topmost window if the DataViewer is null.
createMultipageTIFFDatastore(String, boolean, boolean) - Method in interface org.micromanager.data.DataManager: Generate a new, "blank" Datastore with multipage TIFF-based Storage and return it.
createMultipageTIFFDatastore(Datastore, String, boolean, boolean) - Method in interface org.micromanager.data.DataManager
createNDTIFFDatastore(String) - Method in interface org.micromanager.data.DataManager: Generate a new, "blank" Datastore with NDTIFF-based Storage and return it.
createNDTIFFDatastore(Datastore, String) - Method in interface org.micromanager.data.DataManager
createOverlay() - Method in interface org.micromanager.display.overlay.OverlayPlugin
createPanelController(Studio) - Method in interface org.micromanager.display.inspector.InspectorPanelPlugin
createPipeline(List<ProcessorFactory>, Datastore, boolean) - Method in interface org.micromanager.data.DataManager: Create a new Pipeline using the provided list of ProcessorFactories.
createProcessor(Image) - Method in interface org.micromanager.data.ImageJConverter: Create an ImageProcessor whose image pixel data is derived from the provided Image.
createProcessor() - Method in interface org.micromanager.data.ProcessorFactory: Generate a new DataProcessor based on the configuration of the Factory.
createProcessorFromComponent(Image, int) - Method in interface org.micromanager.data.ImageJConverter: Create an ImageProcessor whose image pixel data is derived from a single component of the provided Image.
createRAMDatastore() - Method in interface org.micromanager.data.DataManager: Generate a new, "blank" Datastore with RAM-based Storage and return it.
createRAMDatastore(Datastore) - Method in interface org.micromanager.data.DataManager
createRewritableRAMDatastore() - Method in interface org.micromanager.data.DataManager: Generate a new, "blank" RewritableDatastore with RAM-based Storage and return it.
createRewritableRAMDatastore(Datastore) - Method in interface org.micromanager.data.DataManager
createSinglePlaneTIFFSeriesDatastore(String) - Method in interface org.micromanager.data.DataManager: Generate a new, "blank" Datastore whose Storage is a series of single-plane TIFF files.
createSinglePlaneTIFFSeriesDatastore(Datastore, String) - Method in interface org.micromanager.data.DataManager
CUSTOM_ICON_STRING - Static variable in class org.micromanager.quickaccess.WidgetPlugin: Key used for custom icon information.
customIntervalsMs(ArrayList<Double>) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
customIntervalsMs - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and customIntervalsMs() instead
customIntervalsMs() - Method in class org.micromanager.acquisition.SequenceSettings: Time intervals between the starts of time points in milliseconds.
customIntervalsMs(double...) - Method in interface org.micromanager.data.SummaryMetadata.Builder
customIntervalsMs(Iterable<Double>) - Method in interface org.micromanager.data.SummaryMetadata.Builder
customIntervalsMs(Double[]) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.

D

data() - Method in interface org.micromanager.Studio: Provide access to the DataManager instance for accessing Micro-Manager data constructs.
DataManager - Interface in org.micromanager.data: This class provides general utility functions for working with Micro-Manager data.
DataProvider - Interface in org.micromanager.data: Read-only access to multi-dimensional image data.
DataProviderHasNewImageEvent - Interface in org.micromanager.data: This class signifies that an image has been added to a DataProvider.
DataProviderHasNewNameEvent - Interface in org.micromanager.data: This event posts when the DataStore gets a new name, i.e.
DataProviderHasNewSummaryMetadataEvent - Interface in org.micromanager.data: This class signifies that new summary metadata has been set for a DataProvider.
Datastore - Interface in org.micromanager.data: Read/write access to multi-dimensional image data.
Datastore.SaveMode - Enum in org.micromanager.data: The file format to save to.
DatastoreClosingEvent - Interface in org.micromanager.data: This class signifies that a Datastore's close() method has been called, and thus that all resources associated with that Datastore, and references to the Datastore, should be removed so that it can be garbage collected.
DatastoreFrozenEvent - Interface in org.micromanager.data: This class signifies that a Datastore has become frozen and can no longer be written to (but read actions may still occur).
DatastoreFrozenException - Exception in org.micromanager.data: An unchecked exception thrown when an attempt is made to modify a Datastore that has been frozen.
DatastoreFrozenException() - Constructor for exception org.micromanager.data.DatastoreFrozenException
DatastoreRewriteException - Exception in org.micromanager.data: An unchecked exception thrown when an attempt is made to overwrite data in a non-rewritable datastore.
DatastoreRewriteException() - Constructor for exception org.micromanager.data.DatastoreRewriteException
DataViewer - Interface in org.micromanager.display: General interface for any user interface displaying image data.
DataViewerListener - Class in org.micromanager.display: Simple interface dedicated to the question if a dataviewer can be closed or not.
DataViewerListener() - Constructor for class org.micromanager.display.DataViewerListener
deleteAllImages() - Method in interface org.micromanager.data.RewritableDatastore: Delete all images from the Datastore.
deleteImage(Coords) - Method in interface org.micromanager.data.RewritableDatastore: Delete an image from the Datastore.
deleteImage(Coords) - Method in interface org.micromanager.data.RewritableStorage: Delete an image from the Storage.
deleteImagesMatching(Coords) - Method in interface org.micromanager.data.RewritableDatastore: Delete all images from the Datastore whose coordinates match the provided Coords object, which may be underspecified.
detachDataViewer() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController: Detach from any currently attached data viewer.
detachDataViewer() - Method in interface org.micromanager.display.inspector.InspectorPanelController
directory(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
directory(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
dismiss() - Method in interface org.micromanager.alerts.Alert: Dismiss the Alert, causing it to no longer be visible to the user.
DisplayDidShowImageEvent - Interface in org.micromanager.display: This event posts when a DataViewer displays an image(s).
DisplayGearMenuPlugin - Interface in org.micromanager.display: DisplayGearMenuPlugins add items to be shown in the "gear menu" shown in each DisplayWindow.
displayImage(Image) - Method in interface org.micromanager.SnapLiveManager: Insert the provided image into the Datastore, causing it to be displayed in any open Snap/Live DisplayWindows.
DisplayManager - Interface in org.micromanager.display: This interface declares generic display-related methods.
DisplayPositionChangedEvent - Interface in org.micromanager.display: This event posts when the position (i.e., Channel, Time, Position, Slice, possibly other Axes) in the display changed.
displays() - Method in interface org.micromanager.Studio: Provides access to the DisplayManager instance for accessing Micro-Manager display constructs.
DisplaySettings - Interface in org.micromanager.display: This class defines the parameters that control how a given DisplayWindow displays data from the Datastore.
DisplaySettings.Builder - Interface in org.micromanager.display: Builder for DisplaySettings.
DisplaySettings.ColorMode - Enum in org.micromanager.display: ColorMode enums.
DisplaySettings.ContrastSettings - Interface in org.micromanager.display: Deprecated.
TODO: explain
DisplaySettings.DisplaySettingsBuilder - Interface in org.micromanager.display: Deprecated.
Use DisplaySettings.Builder instead
displaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager: Generate a "blank" DisplaySettings.Builder with all null values.
DisplaySettingsChangedEvent - Interface in org.micromanager.display: Event used internally by a data viewer to respond to requests to update the display settings.
displayStatusString(String) - Method in interface org.micromanager.display.DisplayWindow: Display a custom string in the window.
displayTimeUnit(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
displayTimeUnit() - Method in class org.micromanager.acquisition.SequenceSettings: Time unit, only used to store preferred way to display the time.
DisplayWindow - Interface in org.micromanager.display: A DisplayWindow is the interface to Micro-Manager's image display windows.
DisplayWindowControlsFactory - Interface in org.micromanager.display: A ControlsFactory is used to provide custom controls for a DisplayWindow.
dispose() - Method in class org.micromanager.display.AbstractDataViewer: Must be called by implementation to release resources.
doZStack(Boolean) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
doZStack - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
doZStack() - Method in class org.micromanager.acquisition.ChannelSpec
duplicate() - Method in interface org.micromanager.display.DisplayWindow: Create a new display window for the same data provider as this one.

E

elapsedTimeMs(Double) - Method in interface org.micromanager.data.Metadata.Builder
elapsedTimeMs(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
emptyPropertyMap() - Method in interface org.micromanager.PropertyManager: Returns an empty property map.
emptyPropertyMap() - Static method in class org.micromanager.PropertyMaps: Return the empty property map.
enableContinuousFocus(boolean) - Method in interface org.micromanager.AutofocusPlugin: Turns on continuous autofocus.
equals(Object) - Method in class org.micromanager.MultiStagePosition: Compares this MultiStagePosition to another, and returns true if they are equal in all aspects.
equals(Object) - Method in class org.micromanager.StagePosition: Compare us against the provided StagePosition and return true only if we are equal in all respects.
ERROR_MESSAGE - Static variable in exception org.micromanager.data.DatastoreFrozenException
ERROR_MESSAGE - Static variable in exception org.micromanager.data.DatastoreRewriteException
EventManager - Interface in org.micromanager.events: This interface provides access to the application-wide EventBus, on which the events in the org.micromanager.events package are posted.
EventPublisher - Interface in org.micromanager: Any object that bears an internal event bus to which other objects can subscribe to receive events.
events() - Method in interface org.micromanager.Studio: Provides access to the EventManager instance for subscribing to and posting events on the application-wide EventBus.
export() - Method in interface org.micromanager.display.ImageExporter: Run the export process.
exposure(double) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
exposure - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
exposure() - Method in class org.micromanager.acquisition.ChannelSpec
ExposureChangedEvent - Interface in org.micromanager.events: This class signals when the exposure time for a given camera has changed.
exposureMs(Double) - Method in interface org.micromanager.data.Metadata.Builder
exposureMs(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
extremaPercentage(Double) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.

F

fileName(String) - Method in interface org.micromanager.data.Metadata.Builder
FILENAME - Static variable in interface org.micromanager.display.DisplaySettings: Deprecated.
fireInspectorPanelDidChangeHeight() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
fireInspectorPanelDidChangeTitle() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
fireInspectorPanelWillChangeHeight() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
fireOverlayConfigurationChanged() - Method in class org.micromanager.display.overlay.AbstractOverlay: Call this method to notify the system that the overlay has changed.
fireOverlayTitleChanged() - Method in class org.micromanager.display.overlay.AbstractOverlay: Call this method to notify the system that the overlay title has changed.
freeze() - Method in interface org.micromanager.data.Datastore: Freeze this Datastore so it cannot be further modified.
freeze() - Method in interface org.micromanager.data.Storage: Freeze the Storage, preventing any changes to its contents.
fromInt(int) - Static method in enum org.micromanager.display.DisplaySettings.ColorMode: Deprecated.
fromJSON(String) - Method in interface org.micromanager.PropertyManager: Creates a property map from its JSON-serialized form.
fromJSON(String) - Static method in class org.micromanager.PropertyMaps: Create a property map from its JSON-serialized form.
fromJSONStream(String) - Static method in class org.micromanager.acquisition.ChannelSpec: De-serialize from JSON encoded string.
fromJSONStream(String) - Static method in class org.micromanager.acquisition.SequenceSettings
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.data.Coordinates: Constructs a Coords instance from a PropertyMap.
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.MultiStagePosition: Generates a multistagePosition from the given PropertyMap.
fromPropertyMap(PropertyMap) - Static method in class org.micromanager.StagePosition: Returns the given PrropertyMap as a StagePosition.
fromString(String) - Static method in enum org.micromanager.ApplicationSkin.SkinMode: Returns skinmode associated with the given string (if any).
fullFocus() - Method in interface org.micromanager.AutofocusPlugin: Runs a full, one-shot autofocus protocol.

G

generateLabel() - Method in class org.micromanager.PositionList: Helper method to generate unique label when inserting a new position.
generateLabel(String) - Method in class org.micromanager.PositionList: Generates a label for a new Position.
generateMetadata(Image, boolean) - Method in interface org.micromanager.acquisition.AcquisitionManager: Generate a new Metadata that contains pre-populated fields based on the current state of the program and the provided Image.
generateSummaryMetadata() - Method in interface org.micromanager.acquisition.AcquisitionManager: Generate a new SummaryMetadata that contains pre-populated fields based on the current state of the program.
generateUUID() - Method in interface org.micromanager.data.Metadata.Builder
get(int) - Method in class org.micromanager.MultiStagePosition: Return stage position based on index.
get(String) - Method in class org.micromanager.MultiStagePosition: Returns position for a specific stage.
get1DPosition() - Method in class org.micromanager.StagePosition
get2DPositionX() - Method in class org.micromanager.StagePosition
get2DPositionY() - Method in class org.micromanager.StagePosition
getAcquisitionManager() - Method in interface org.micromanager.Studio: Provide access to the AcquisitionManager, for running data acquisition using the Micro-Manager acquisition engine.
getAcquisitionSettings() - Method in interface org.micromanager.acquisition.AcquisitionManager: Return current acquisition settings as shown in the Multi-D Acquisition dialog.
getActiveDataViewer() - Method in interface org.micromanager.display.DisplayManager: Returns the currently active data viewer.
getAffineTransform(String, AffineTransform) - Method in interface org.micromanager.PropertyMap
getAffineTransform(String, AffineTransform) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getAffineTransformList(String, AffineTransform...) - Method in interface org.micromanager.PropertyMap
getAffineTransformList(String, Iterable<AffineTransform>) - Method in interface org.micromanager.PropertyMap
getAffineTransformList(String, AffineTransform...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getAffineTransformList(String, Iterable<AffineTransform>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getAlbum() - Method in interface org.micromanager.Studio: Provides access to and control of the contents of the Album, the implicit, temporary image storage datastore.
getAlertManager() - Method in interface org.micromanager.Studio: Provide access to the AlertManager, for creating low-profile, non- interrupting alerts in the user interface.
getAllAutofocusMethods() - Method in interface org.micromanager.AutofocusManager: Return a list of the current valid autofocus names, suitable for use in setAutofocusMethodByName().
getAllChannelColors() - Method in interface org.micromanager.display.DisplaySettings
getAllChannelSettings() - Method in interface org.micromanager.display.DisplaySettings
getAllChannelVisibilities() - Method in interface org.micromanager.display.DisplaySettings
getAllComponentSettings() - Method in interface org.micromanager.display.ChannelDisplaySettings
getAllDataViewers() - Method in interface org.micromanager.display.DisplayManager: Return all DataViewers that Micro-Manager knows about.
getAllImageWindows() - Method in interface org.micromanager.display.DisplayManager: Return all active DisplayWindows.
getAnnotation(String) - Method in interface org.micromanager.data.Datastore: Get an annotation, creating it if it doesn't exist.
getAnyImage() - Method in interface org.micromanager.data.DataProvider: Retrieve any image from this DataProvider.
getAnyImage() - Method in interface org.micromanager.data.Storage: Return any Image, or null if there are no images.
getApplication() - Method in interface org.micromanager.Studio: Provides access to the application API for controlling and updating the GUI.
getApplicationPipelineConfigurators(boolean) - Method in interface org.micromanager.data.DataManager: Return a list of the ProcessorConfigurators currently being used by the application pipeline interface.
getApplicationSkin() - Method in interface org.micromanager.Application: Provides access to the application skin API for determining colors for various GUI components.
getAsNumber(String, Number) - Method in interface org.micromanager.PropertyMap: Retrieve a numerical value, without checking its specific type.
getAsNumber(String, Number) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getAsNumberList(String, Number...) - Method in interface org.micromanager.PropertyMap
getAsNumberList(String, Iterable<Number>) - Method in interface org.micromanager.PropertyMap
getAsNumberList(String, Number...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getAsNumberList(String, Iterable<Number>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getAsOpaqueValue(String) - Method in interface org.micromanager.PropertyMap
getAsWindow() - Method in interface org.micromanager.display.DisplayWindow: Deprecated.
use DisplayWindow.getWindow() instead
getAutofocusManager() - Method in interface org.micromanager.Studio: Provide access to the AutofocusManager, for performing autofocus operations.
getAutofocusMethod() - Method in interface org.micromanager.AutofocusManager: Return the current AutofocusPlugin being used to run autofocus.
getAutofocusPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to AutofocusPlugin instances.
getAutoscaleIgnoredPercentile() - Method in interface org.micromanager.display.DisplaySettings: When autoscaling, the minimum value will have this fraction of pixels with lower intensities, and the maximum value will have this fraction of pixels with higher intensities.
getAutoscaleIgnoredQuantile() - Method in interface org.micromanager.display.DisplaySettings: When autoscaling, the minimum value will have this fraction of pixels with lower intensities, and the maximum value will have this fraction of pixels with higher intensities.
getAutoShutter() - Method in interface org.micromanager.events.AutoShutterEvent: Returns true when autoshutter is enabled, false otherwise.
getAutoShutter() - Method in interface org.micromanager.ShutterManager: Return true if autoshutter is enabled.
getAxes() - Method in interface org.micromanager.data.Coords: Return all axes that this Coords has an index for.
getAxes() - Method in interface org.micromanager.data.DataProvider: Retrieve the axis currently in use by this DataProvider.
getAxes() - Method in interface org.micromanager.data.Storage: Return a List of all axis names for Images we know about.
getAxisLength(String) - Method in interface org.micromanager.data.DataProvider: Deprecated.
Use DataProvider.getNextIndex(String) instead.
getAxisOrder() - Method in interface org.micromanager.data.SummaryMetadata: Deprecated.
- Use getOrdereddAxes() instead
getBackgroundColor() - Method in interface org.micromanager.ApplicationSkin: Return the current background color for normal GUI elements.
getBinning() - Method in interface org.micromanager.data.Metadata: The binning mode of the camera for this image.
getBinSize() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the number of distinct intensities that fit within each bin of the histogram.
getBitDepth() - Method in interface org.micromanager.data.Metadata: The number of bits used to represent each pixel (e.g.
getBitDepth() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the bit depth of the dataset.
getBoolean(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getBoolean(String, Boolean) - Method in interface org.micromanager.PropertyMap: Deprecated.
getBoolean(String, boolean) - Method in interface org.micromanager.PropertyMap
getBoolean(String, boolean) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getBoolean(Class<?>, String, Boolean) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getBoolean(key, fallback) instead
getBooleanArray(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getBooleanArray(String, Boolean[]) - Method in interface org.micromanager.PropertyMap: Deprecated.
getBooleanArray(Class<?>, String, Boolean[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getBooleanList(key, fallback) instead
getBooleanList(String, boolean...) - Method in interface org.micromanager.PropertyMap
getBooleanList(String, Iterable<Boolean>) - Method in interface org.micromanager.PropertyMap
getBooleanList(String, boolean...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getBooleanList(String, Iterable<Boolean>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getButtonIcon() - Method in class org.micromanager.quickaccess.SimpleButtonPlugin: Returns an icon to show in the button.
getByte(String, byte) - Method in interface org.micromanager.PropertyMap
getByte(String, byte) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getByteArray() - Method in interface org.micromanager.data.Image: Regardless of the the value of #getBytesPerPixel return an array of bytes containing raw data for the image.
getByteList(String, byte...) - Method in interface org.micromanager.PropertyMap
getByteList(String, Iterable<Byte>) - Method in interface org.micromanager.PropertyMap
getByteList(String, byte...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getByteList(String, Iterable<Byte>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getBytesPerComponent() - Method in interface org.micromanager.data.Image: Return the number of bytes used to represent each pixel component of this image.
getBytesPerPixel() - Method in interface org.micromanager.data.Image: Return the number of bytes used to represent each pixel of this image.
getC() - Method in interface org.micromanager.data.Coords: Shorthand for getChannel.
getCamera() - Method in interface org.micromanager.data.Metadata: The name of the camera for this image.
getCameraName() - Method in interface org.micromanager.events.ExposureChangedEvent: Camera whose exposure time changed.
getCameraTransform(String) - Method in interface org.micromanager.CompatibilityInterface: Deprecated.
- Use core.getPixelSizeAffineByID(config) instead
getCanCustomizeIcon() - Method in class org.micromanager.quickaccess.WidgetPlugin: Returns true if the widget can accept custom icons (i.e.
getChannel() - Method in interface org.micromanager.data.Coords: Get the channel index.
getChannel() - Method in interface org.micromanager.events.ChannelExposureEvent: Return the channel whose exposure time has changed.
getChannelColor(int) - Method in interface org.micromanager.display.DisplaySettings
getChannelColorMode() - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
- use getColorMode() instead
getChannelContrastSettings() - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
getChannelExposureTime(String, String, double) - Method in interface org.micromanager.Application: Retrieve the exposure time that has been set for the specified channel.
getChannelGroup() - Method in interface org.micromanager.data.SummaryMetadata: The config group that was used to switch between channels.
getChannelGroup() - Method in interface org.micromanager.events.ChannelExposureEvent: Return the name of the channel group in which the modified channel is located.
getChannelNameList() - Method in interface org.micromanager.data.SummaryMetadata
getChannelNames() - Method in interface org.micromanager.data.SummaryMetadata: Deprecated.
- Use getChannelNameList() instead
getChannelSettings(int) - Method in interface org.micromanager.display.DisplaySettings.Builder: Returns the ChannelDisplaySettings for the given channel number.
getChannelSettings(int) - Method in interface org.micromanager.display.DisplaySettings
getCMMCore() - Method in interface org.micromanager.Studio: Provides access to the Core and its functionality.
getColor() - Method in interface org.micromanager.display.ChannelDisplaySettings: Color used to represent this channel, i.e., brightest color of the LUT used to display this channel
getColor(String, Color) - Method in interface org.micromanager.PropertyMap
getColor(String, Color) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getColorList(String, Color...) - Method in interface org.micromanager.PropertyMap
getColorList(String, Iterable<Color>) - Method in interface org.micromanager.PropertyMap
getColorList(String, Color...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getColorList(String, Iterable<Color>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getColorMode() - Method in interface org.micromanager.display.DisplaySettings: Color mode or lookup table for displaying the image.
getCompatibilityInterface() - Method in interface org.micromanager.Studio: Provides access to the compatibility layer that exposes some old 1.4 API methods.
getComponentIntensitiesAt(int, int) - Method in interface org.micromanager.data.Image: Returns the pixel intensity of all components.
getComponentIntensityAt(int, int, int) - Method in interface org.micromanager.data.Image: Get the intensity of a component of the pixel at the specified position.
getComponentSettings(int) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
getComponentSettings(int) - Method in interface org.micromanager.display.ChannelDisplaySettings
getComputerName() - Method in interface org.micromanager.data.SummaryMetadata: The name of the computer the data was collected on.
getConfigFilePaths() - Method in interface org.micromanager.IntroPlugin: Provide a list of paths to config files to include in the config file dropdown menu.
getConfiguration() - Method in class org.micromanager.display.overlay.AbstractOverlay: Return the user-customizable settings for this overlay.
getConfiguration() - Method in interface org.micromanager.display.overlay.Overlay: Return the user-customizable settings for this overlay.
getConfigurationComponent() - Method in class org.micromanager.display.overlay.AbstractOverlay: Return the configuration UI component for this overlay.
getConfigurationComponent() - Method in interface org.micromanager.display.overlay.Overlay: Return the configuration UI component for this overlay.
getContrastGammas() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
getContrastMaxes() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
getContrastMins() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
getContrastSettings(Integer, Integer, Double, Boolean) - Method in interface org.micromanager.display.DisplayManager: Deprecated.
Use DisplaySettings.getAllChannelSettings() instead.
getContrastSettings(Integer[], Integer[], Double[], Boolean) - Method in interface org.micromanager.display.DisplayManager: Deprecated.
getCoords() - Method in interface org.micromanager.data.DataProviderHasNewImageEvent: Returns Coords for the image.
getCoords() - Method in interface org.micromanager.data.Image: Retrieve the Coords of this Image.
getCoordsBuilder() - Method in interface org.micromanager.data.DataManager: Deprecated.
Use DataManager.coordsBuilder() instead
getCopyright() - Method in interface org.micromanager.MMPlugin: Provide a copyright string.
getCurrentFocusScore() - Method in interface org.micromanager.AutofocusPlugin: Returns the current focus "score" (goodness of focus).
getCurrentShutter() - Method in interface org.micromanager.ShutterManager: Return the current shutter device.
getCurrentWindow() - Method in interface org.micromanager.display.DisplayManager: Deprecated.
Use getActiveDataViewer() instead
getCustomIcon(PropertyMap, Icon) - Method in interface org.micromanager.quickaccess.QuickAccessManager: Generate an Icon based on information contained in the provided PropertyMap.
getCustomIntervalsMs() - Method in interface org.micromanager.data.SummaryMetadata: Deprecated.
- Use double[] getCustomIntervalsMsArray() instead
getCustomIntervalsMsArray() - Method in interface org.micromanager.data.SummaryMetadata
getCustomIntervalsMsList() - Method in interface org.micromanager.data.SummaryMetadata: When using a variable amount of time between timepoints, this array has the list of wait times.
getDataManager() - Method in interface org.micromanager.Studio: Provide access to the DataManager instance for accessing Micro-Manager data constructs.
getDataProvider() - Method in interface org.micromanager.data.DataProviderHasNewImageEvent: Provides the DataProvider this image was added to; potentially useful for code that listens to events from multiple DataProviders.
getDataProvider() - Method in interface org.micromanager.display.DataViewer: Retrieve the data provider backing this viewer.
getDatastore() - Method in interface org.micromanager.acquisition.AcquisitionStartedEvent: Return the Datastore into which images will be inserted during the acquisition.
getDatastore() - Method in interface org.micromanager.Album: Return the Datastore that currently backs the Album.
getDatastore() - Method in interface org.micromanager.data.Annotation: Return the datastore to which this annotation is associated.
getDatastore() - Method in interface org.micromanager.data.DatastoreClosingEvent: Returns the Datastore that is closing.
getDatastore() - Method in interface org.micromanager.data.ImageDeletedEvent: Provides the Datastore this image was added to; potentially useful for code that listens to events from multiple Datastores.
getDatastore() - Method in interface org.micromanager.data.ImageOverwrittenEvent: Provides the Datastore this image was added to; potentially useful for code that listens to events from multiple Datastores.
getDatastore() - Method in interface org.micromanager.data.Pipeline: Get the output Datastore for this Pipeline.
getDatastore() - Method in class org.micromanager.display.AbstractDataViewer: Deprecated.
user code should call getDataProvider
getDatastore() - Method in interface org.micromanager.display.DataViewer: Deprecated.
use DataViewer.getDataProvider() instead
getDataViewer() - Method in interface org.micromanager.display.DisplayDidShowImageEvent: Returns the Dataviewer displaying the image.
getDataViewer() - Method in interface org.micromanager.display.DisplayPositionChangedEvent: The dataViewer posting this event.
getDataViewer() - Method in interface org.micromanager.display.DisplaySettingsChangedEvent: Get the data viewer.
getDefaultXYStage() - Method in class org.micromanager.MultiStagePosition: Return the default XY stage, i,e, the one used if no stage is named explicitly.
getDefaultZStage() - Method in class org.micromanager.MultiStagePosition: Returns the Default Z stage, i.e.
getDesc() - Method in enum org.micromanager.ApplicationSkin.SkinMode: Returns a description of this skin.
getDevice() - Method in interface org.micromanager.events.PropertyChangedEvent: Device to which the changed property belongs.
getDeviceName() - Method in interface org.micromanager.events.SLMExposureChangedEvent: Returns name of the SLM device.
getDeviceName() - Method in interface org.micromanager.events.StagePositionChangedEvent: Name of the stage.
getDeviceName() - Method in interface org.micromanager.events.XYStagePositionChangedEvent: Name of the (XYStage) device that change position.
getDimension(String, Dimension) - Method in interface org.micromanager.PropertyMap
getDimension(String, Dimension) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getDimensionList(String, Dimension...) - Method in interface org.micromanager.PropertyMap
getDimensionList(String, Iterable<Dimension>) - Method in interface org.micromanager.PropertyMap
getDimensionList(String, Dimension...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getDimensionList(String, Iterable<Dimension>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getDirectory() - Method in interface org.micromanager.data.SummaryMetadata: The directory the data was originally saved to.
getDisabledBackgroundColor() - Method in interface org.micromanager.ApplicationSkin: Return the current "disabled" background color.
getDisabledTextColor() - Method in interface org.micromanager.ApplicationSkin: Return the current color for disabled text.
getDisplay() - Method in interface org.micromanager.display.DisplaySettingsChangedEvent: Deprecated.
use getDataViewer instead
getDisplay() - Method in interface org.micromanager.SnapLiveManager: Return the DisplayWindow used for snap/live mode.
getDisplayedImages() - Method in interface org.micromanager.display.DataViewer: Retrieve the Images currently being displayed.
getDisplayGearMenuPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to DisplayGearMenuPlugin instances.
getDisplayManager() - Method in interface org.micromanager.Studio: Provides access to the DisplayManager instance for accessing Micro-Manager display constructs.
getDisplayPosition() - Method in class org.micromanager.display.AbstractDataViewer: Implements getDisplayPosition.
getDisplayPosition() - Method in interface org.micromanager.display.DataViewer: Get the coordinates for the currently displayed images.
getDisplayPosition() - Method in interface org.micromanager.display.DisplayPositionChangedEvent: returns the new display position.
getDisplays(Datastore) - Method in interface org.micromanager.display.DisplayManager: Deprecated.
replaced by DisplayManager.getDisplays(DataProvider)
getDisplays(DataProvider) - Method in interface org.micromanager.display.DisplayManager: Return all associated DisplayWindows for the DataProvider.
getDisplaySettings() - Method in class org.micromanager.display.AbstractDataViewer: Implements getDisplaySettings.
getDisplaySettings() - Method in interface org.micromanager.display.DataViewer: Get the current display settings.
getDisplaySettings() - Method in interface org.micromanager.display.DisplaySettingsChangedEvent: Get the new display settings.
getDisplaySettingsBuilder() - Method in interface org.micromanager.display.DisplayManager: Deprecated.
- use displaySettingsBuilder() instead
getDouble(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getDouble(String, Double) - Method in interface org.micromanager.PropertyMap: Deprecated.
getDouble(String, double) - Method in interface org.micromanager.PropertyMap
getDouble(String, double) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getDouble(Class<?>, String, Double) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getDouble(key, fallback) instead
getDoubleArray(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getDoubleArray(String, Double[]) - Method in interface org.micromanager.PropertyMap: Deprecated.
getDoubleArray(Class<?>, String, Double[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getDoubleList(key, fallback) instead
getDoubleList(String, double...) - Method in interface org.micromanager.PropertyMap
getDoubleList(String, Iterable<Double>) - Method in interface org.micromanager.PropertyMap
getDoubleList(String, double...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getDoubleList(String, Iterable<Double>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getElapsedTimeMs() - Method in interface org.micromanager.data.Metadata: Deprecated.
- use Double Metadata.getElapsedTimeMs(double) instead
getElapsedTimeMs(double) - Method in interface org.micromanager.data.Metadata: Time in milliseconds since the start of the given data acquisition at which the image was received by Micro-Manager.
getEnabledTextColor() - Method in interface org.micromanager.ApplicationSkin: Return the current color for enabled text.
getEventManager() - Method in interface org.micromanager.Studio: Provides access to the EventManager instance for subscribing to and posting events on the application-wide EventBus.
getExceptions() - Method in interface org.micromanager.data.Pipeline: Return a list containing any exceptions that have occurred during processing of images.
getExposureMs() - Method in interface org.micromanager.data.Metadata: How long of an exposure was used to collect this image.
getFilename() - Method in interface org.micromanager.data.Annotation: Deprecated.
this is an old name for Annotation.getTag()
getFileName() - Method in interface org.micromanager.data.Metadata: The name of the file from which the image was loaded, if applicable.
getFloat(String, float) - Method in interface org.micromanager.PropertyMap
getFloat(String, float) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getFloatList(String, float...) - Method in interface org.micromanager.PropertyMap
getFloatList(String, Iterable<Float>) - Method in interface org.micromanager.PropertyMap
getFloatList(String, float...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getFloatList(String, Iterable<Float>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getGearMenu() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController: Provide a menu used for miscellaneous controls.
getGearMenu() - Method in interface org.micromanager.display.inspector.InspectorPanelController
getGeneralAnnotation() - Method in interface org.micromanager.data.Annotation: Return a PropertyMap of information stored by the Annotation that is not specific to any one image.
getGridColumn() - Method in class org.micromanager.MultiStagePosition: Returns rectangular grid column.
getGridRow() - Method in class org.micromanager.MultiStagePosition: Returns rectangular grid row.
getGroupName() - Method in interface org.micromanager.display.ChannelDisplaySettings: Name of the channelgroup this channel belongs to.
getGroupName() - Method in interface org.micromanager.events.ConfigGroupChangedEvent: Name of the ConfigGroup.
getHeight() - Method in interface org.micromanager.data.Image: Get the height of this image in pixels.
getHelpText() - Method in interface org.micromanager.MMPlugin: Provide a longer string describing the purpose of the plugin.
getHistogram() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the histogram, an array of ints counting the number of samples whose intensities fall into each bin.
getHistoRangeBits() - Method in interface org.micromanager.display.ChannelDisplaySettings: Range of this histogram displayed for this channel For now, histogram always starts at zero, so this represents the maximum value on the x-axis of the histogram.
getIcon() - Method in class org.micromanager.quickaccess.QuickAccessPlugin: Provide an icon to use to represent this plugin when configuring the Quick-Access Window.
getImage(Coords) - Method in interface org.micromanager.data.DataProvider: Returns the image at the given position.
getImage() - Method in interface org.micromanager.data.DataProviderHasNewImageEvent: Provides the newly-added image.
getImage() - Method in interface org.micromanager.data.ImageDeletedEvent: Provides the Image that was deleted.
getImage(Coords) - Method in interface org.micromanager.data.Storage: Retrieve the Image located at the specified coordinates.
getImageAnnotation(Coords) - Method in interface org.micromanager.data.Annotation: Return a PropertyMap of information stored by this Annotation related to the image at the specified coordinates.
getImageHeight() - Method in interface org.micromanager.data.SummaryMetadata: ImageHeight in pixels.
getImageJConverter() - Method in interface org.micromanager.data.DataManager: Provide access to the ImageJConverter() object.
getImageJPixelType() - Method in interface org.micromanager.data.Image: Deprecated.
Unclear what should be used instead. Do not delete until this is figure out.
getImageNumber() - Method in interface org.micromanager.data.Metadata: The sequence number of this image, for sequence acquisitions.
getImagePlus() - Method in interface org.micromanager.display.DisplayWindow: Deprecated.
Directly accessing the ImagePlus of an MMStudio display window will generally result in very fragile code. Consider accessing image data through DataViewer.getDataProvider(). For drawing overlay graphics, see DisplayWindow.addOverlay(org.micromanager.display.overlay.Overlay).
getImages() - Method in interface org.micromanager.display.DisplayDidShowImageEvent: Returns the images newly displayed.
getImagesIgnoringAxes(Coords, String...) - Method in interface org.micromanager.data.DataProvider: Returns a list of image in the DataProvider's collection that have identical coords after removing the given axes from both source and target.
getImagesIgnoringAxes(Coords, String...) - Method in interface org.micromanager.data.Storage: Retrieve a list of images with Coords identical to the given Coords instance, except for the axes listed in the exception list.
getImagesMatching(Coords) - Method in interface org.micromanager.data.DataProvider: Deprecated.
- instead use getImagesIgnoringAxes
getImagesMatching(Coords) - Method in interface org.micromanager.data.Storage: Retrieve a list of all images whose Coords match the given incomplete Coords instance.
getImageWidth() - Method in interface org.micromanager.data.SummaryMetadata: ImageWidth in pixels.
getIndex(String) - Method in interface org.micromanager.data.Coords: Get the index for the given axis.
getIndex() - Method in enum org.micromanager.display.DisplaySettings.ColorMode: Deprecated.
getInspectorPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to InspectorPlugin instances.
getInt(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getInt(String, Integer) - Method in interface org.micromanager.PropertyMap: Deprecated.
getInt(Class<?>, String, Integer) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getInteger(key, fallback) instead
getIntArray(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getIntArray(String, Integer[]) - Method in interface org.micromanager.PropertyMap: Deprecated.
getIntArray(Class<?>, String, Integer[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getIntegerList(key, fallback) instead
getInteger(String, int) - Method in interface org.micromanager.PropertyMap
getInteger(String, int) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getIntegerList(String, int...) - Method in interface org.micromanager.PropertyMap
getIntegerList(String, Iterable<Integer>) - Method in interface org.micromanager.PropertyMap
getIntegerList(String, int...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getIntegerList(String, Iterable<Integer>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getIntendedDimensions() - Method in interface org.micromanager.data.SummaryMetadata: The expected number of images along each axis that were to be collected.
getIntensityAt(int, int) - Method in interface org.micromanager.data.Image: Retrieve the intensity of the pixel at the specified position.
getIntensityStringAt(int, int) - Method in interface org.micromanager.data.Image: Generate a string describing the value(s) of the pixel at the specified location.
getIntroPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to IntroPlugin instances.
getIsCancelled() - Method in interface org.micromanager.events.ShutdownCommencingEvent: Deprecated.
use ShutdownCommencingEvent.isCanceled() instead
getIsLiveModeOn() - Method in interface org.micromanager.SnapLiveManager: Deprecated.
getIsMainExposureTime() - Method in interface org.micromanager.events.ChannelExposureEvent: Deprecated.
use ChannelExposureEvent.isMainExposureTime() instead
getIsManaged(DataProvider) - Method in interface org.micromanager.display.DisplayManager: Deprecated.
use DisplayManager.isManaged(DataProvider) instead
getIsOn() - Method in interface org.micromanager.events.LiveModeEvent: Deprecated.
use LiveModeEvent.isOn() instead.
getIsSynchronous() - Method in interface org.micromanager.data.Pipeline: Deprecated.
Use Pipeline.isSynchronous() instead.
getIsVisible() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
Use DisplaySettings.ContrastSettings.isVisible()
getKeepShutterOpenChannels() - Method in interface org.micromanager.data.SummaryMetadata: For acquisitions with more than one channel, whether or not the shutter was left open in between each channel.
getKeepShutterOpenSlices() - Method in interface org.micromanager.data.SummaryMetadata: For acquisitions with more than one Z slice, whether or not the shutter was left open in between each slice.
getKeys() - Method in interface org.micromanager.PropertyMap: Deprecated.
getLabel() - Method in class org.micromanager.MultiStagePosition: Returns position label.
getLightBackgroundColor() - Method in interface org.micromanager.ApplicationSkin: Return the current "lighter" background color for highlighted or otherwise differentiated GUI elements.
getLivePipelineConfigurators(boolean) - Method in interface org.micromanager.data.DataManager: Return a list of the ProcessorConfigurators currently being used by the live pipeline interface.
getLogManager() - Method in interface org.micromanager.Studio: Provides access to Micro-Manager's logging functions, like logError(), showMessage(), etc.
getLong(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getLong(String, Long) - Method in interface org.micromanager.PropertyMap: Deprecated.
getLong(String, long) - Method in interface org.micromanager.PropertyMap
getLong(String, long) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getLong(Class<?>, String, Long) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getLong(key, fallback) instead
getLongArray(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getLongArray(String, Long[]) - Method in interface org.micromanager.PropertyMap: Deprecated.
getLongArray(Class<?>, String, Long[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getLongList(key, fallback) instead
getLongList(String, long...) - Method in interface org.micromanager.PropertyMap
getLongList(String, Iterable<Long>) - Method in interface org.micromanager.PropertyMap
getLongList(String, long...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getLongList(String, Iterable<Long>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getMagnification() - Method in interface org.micromanager.display.DisplayWindow: Deprecated.
use DisplayWindow.getZoom() instead
getMainWindow() - Method in interface org.micromanager.Application: Provide access to the main window of the program.
getManagedDataProviders() - Method in interface org.micromanager.display.DisplayManager: Return a list of all DataProviders that MicroManager is managing (see the manage() method for more information).
getMaxIgnoringOutliers() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the intensity of the brightest sample in the dataset once a fraction of all pixels have been discarded.
getMaxIndex(String) - Method in interface org.micromanager.data.Storage: Return the largest stored position along the specified axis.
getMaxIndices() - Method in interface org.micromanager.data.DataProvider: Deprecated.
Use DataProvider.getNextIndex(String axis) instead
getMaxIndices() - Method in interface org.micromanager.data.Storage: Return a Coords that provides the maximum index along all available axes.
getMaxVal() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the intensity of the brightest sample in the dataset used to generate the histogram.
getMean() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the mean value of all samples in the dataset.
getMenuPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to MenuPlugin instances.
getMetadata() - Method in interface org.micromanager.data.Image: Retrieve the Metadata for this Image.
getMetadataBuilder() - Method in interface org.micromanager.data.DataManager: Deprecated.
Use DataManager.metadataBuilder() instead
getMetadataVersion() - Method in interface org.micromanager.data.SummaryMetadata: The version of the metadata when the data was collected.
getMicroManagerVersion() - Method in interface org.micromanager.data.SummaryMetadata: The version of Micro-Manager used to collect the data.
getMinIgnoringOutliers() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the intensity of the dimmest sample in the dataset once a fraction of all pixels have been discarded.
getMinVal() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the intensity of the dimmest sample in the dataset used to generate the histogram.
getName() - Method in interface org.micromanager.data.DataProvider: A dataProvider has a name (not guaranteed to be unique).
getName() - Method in interface org.micromanager.display.ChannelDisplaySettings: Returns name of the channel that is displayed.
getName() - Method in interface org.micromanager.display.DataViewer: Return the name of this viewer.
getName() - Method in interface org.micromanager.MMPlugin: Provide a short string identifying the plugin.
getNewChannelGroup() - Method in interface org.micromanager.events.ChannelGroupChangedEvent: Provides the name of the newly selected channel group.
getNewConfig() - Method in interface org.micromanager.events.ConfigGroupChangedEvent: Returns the name of the newly selected config in the group.
getNewExposureTime() - Method in interface org.micromanager.events.ChannelExposureEvent: Return the new exposure time for the channel.
getNewExposureTime() - Method in interface org.micromanager.events.ExposureChangedEvent: New exposure time.
getNewExposureTime() - Method in interface org.micromanager.events.SLMExposureChangedEvent: Returns new exposure time of the SLM.
getNewImage() - Method in interface org.micromanager.data.ImageOverwrittenEvent: Provides the newly-added image.
getNewName() - Method in interface org.micromanager.data.DataProviderHasNewNameEvent: Returns the new name of the DataProvider.
getNewPixelSizeAffine() - Method in interface org.micromanager.events.PixelSizeAffineChangedEvent: New affine transform.
getNewPixelSizeUm() - Method in interface org.micromanager.events.PixelSizeChangedEvent: New pixels size in microns.
getNewSettings() - Method in interface org.micromanager.acquisition.AcquisitionSettingsChangedEvent: Return the freshly changed SequenceSettings.
getNextIndex(String) - Method in interface org.micromanager.data.DataProvider: Returns the highest index along the given axis plus 1.
getNumberOfChannels() - Method in interface org.micromanager.display.DisplaySettings.Builder: Number of ChannelDisplaySettings in this builder.
getNumberOfChannels() - Method in interface org.micromanager.display.DisplaySettings: Returns the number of channels in these DisplaySettings Note that this number may be different from the number of the channels in the image being shown.
getNumberOfComponents() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
getNumberOfComponents() - Method in interface org.micromanager.display.ChannelDisplaySettings
getNumberOfImages() - Method in interface org.micromanager.AutofocusPlugin: Returns the number of images acquired.
getNumberOfPositions() - Method in class org.micromanager.PositionList: Returns the number of positions contained within the list.
getNumberOfStageAxes() - Method in class org.micromanager.StagePosition
getNumComponents() - Method in interface org.micromanager.data.Image: Get the number of components per pixel in this image.
getNumComponents() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
getNumImages() - Method in interface org.micromanager.data.DataProvider: Provides total number of images that can be accessed through this DataProvider.
getNumImages() - Method in interface org.micromanager.data.Storage: Return the number of images in this dataset.
getNumSamples() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the number of samples used to construct the histogram.
getOldImage() - Method in interface org.micromanager.data.ImageOverwrittenEvent: Provides the image that was overwritten.
getOrderedAxes() - Method in interface org.micromanager.data.SummaryMetadata: The order in which axes changed when adding images to the dataset.
getOverlayPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to OverlayPlugin instances.
getOverlays() - Method in interface org.micromanager.display.DisplayWindow: Get the overlays attached to this display.
getP() - Method in interface org.micromanager.data.Coords: Shorthand for getStagePosition.
getPaddedCellSize() - Static method in class org.micromanager.quickaccess.QuickAccessPlugin: Provides a dimension that mostly fills 1 cell in the Quick-Access Window.
getPanel() - Method in interface org.micromanager.display.inspector.InspectorPanelController
getPanels() - Method in interface org.micromanager.quickaccess.QuickAccessManager: Retrieve a mapping of Quick Access Panel titles to the panels themselves.
getPixelAspect() - Method in interface org.micromanager.data.Metadata: The aspect ratio of the pixels in this image, as a Y/X ratio (e.g.
getPixelSizeAffine() - Method in interface org.micromanager.data.Metadata: Geometric relation between stage movement (in microns) and pixels.
getPixelSizeUm() - Method in interface org.micromanager.data.Metadata: How much of the sample, in microns, a single pixel of the camera sees.
getPlaybackFPS() - Method in interface org.micromanager.display.DisplaySettings
getPluginManager() - Method in interface org.micromanager.Studio: Provides access to the PluginManager for accessing plugin instances.
getPoint(String, Point) - Method in interface org.micromanager.PropertyMap
getPoint(String, Point) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getPointList(String, Point...) - Method in interface org.micromanager.PropertyMap
getPointList(String, Iterable<Point>) - Method in interface org.micromanager.PropertyMap
getPointList(String, Point...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getPointList(String, Iterable<Point>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getPos() - Method in interface org.micromanager.events.StagePositionChangedEvent: Position of the stage.
getPosition(int) - Method in class org.micromanager.PositionList: Returns multi-stage position associated with the position index.
getPositionCopy(int) - Method in class org.micromanager.PositionList: Returns a copy of the multi-stage position associated with the position index.
getPositionIndex(String) - Method in class org.micromanager.PositionList: Returns position index associated with the position name.
getPositionList() - Method in interface org.micromanager.events.NewPositionListEvent: Returns the new stage position list.
getPositionList() - Method in interface org.micromanager.PositionListManager: Returns a copy of the current PositionList, the one used by the Acquisition Protocol.
getPositionListManager() - Method in interface org.micromanager.Studio: Provides access to the PositionListManager for interacting with the Stage Position List.
getPositionName() - Method in interface org.micromanager.data.Metadata: Deprecated.
Use Metadata.getPositionName(java.lang.String) instead
getPositionName(String) - Method in interface org.micromanager.data.Metadata: Any name attached to the stage position at which this image was acquired.
getPositions() - Method in class org.micromanager.PositionList: Returns an array of positions contained in the list.
getPreferredSaveMode() - Method in interface org.micromanager.data.DataManager: Return the save mode that the user prefers to use.
getPrefix() - Method in interface org.micromanager.data.SummaryMetadata: The user-supplied portion of the filename, plus any additional numerical identifier needed to ensure uniqueness.
getPreviousDisplayPosition() - Method in interface org.micromanager.display.DisplayPositionChangedEvent: Returns the previously displayed position.
getPreviousDisplaySettings() - Method in interface org.micromanager.display.DisplaySettingsChangedEvent: Get the display settings before the change being handled.
getPrimaryImage() - Method in interface org.micromanager.display.DisplayDidShowImageEvent: Unsure what this is or means.
getProcessorPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to ProcessorPlugin instances.
getProcessors() - Method in interface org.micromanager.data.Pipeline: Return the list of Processors used by this Pipeline.
getProfileName() - Method in interface org.micromanager.data.SummaryMetadata: The name of the Micro-Manager profile used to collect this data.
getProfileName() - Method in interface org.micromanager.UserProfile: Returns the name of this profile as displayed to the user.
getProperties() - Method in interface org.micromanager.AutofocusPlugin: Returns an array of the properties for this autofocus plugin.
getProperty(String) - Method in interface org.micromanager.AutofocusPlugin: Returns the name and value of properties for the autofocus plugin.
getProperty() - Method in interface org.micromanager.events.PropertyChangedEvent: Returns the property key.
getProperty(String) - Method in class org.micromanager.MultiStagePosition: Returns property value for a given key (name).
getPropertyManager() - Method in interface org.micromanager.Studio: Provides access to the PropertyManagerAPI.
getPropertyMap(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getPropertyMap(String, PropertyMap) - Method in interface org.micromanager.PropertyMap
getPropertyMap(String, PropertyMap) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getPropertyMapBuilder() - Method in interface org.micromanager.data.DataManager: Deprecated.
Use PropertyMaps.builder() instead
getPropertyMapBuilder() - Method in interface org.micromanager.display.DisplayManager: Deprecated.
Use PropertyMaps.builder() instead
getPropertyMapList(String, PropertyMap...) - Method in interface org.micromanager.PropertyMap
getPropertyMapList(String, Iterable<PropertyMap>) - Method in interface org.micromanager.PropertyMap
getPropertyMapList(String, PropertyMap...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getPropertyMapList(String, Iterable<PropertyMap>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getPropertyNames() - Method in interface org.micromanager.AutofocusPlugin: Returns an array of the names of properties for this autofocus plugin.
getPropertyNames() - Method in class org.micromanager.MultiStagePosition: Return the array of property keys (names) associated with this position.
getPropertyType(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getPropertyValue(String) - Method in interface org.micromanager.AutofocusPlugin: Gets the value of a named property.
getQuickAccessManager() - Method in interface org.micromanager.Studio: Provides access to the QuickAccessManager for accessing the Quick-Access Panel system.
getQuickAccessPlugins() - Method in interface org.micromanager.PluginManager: Return a HashMap that maps plugin class names to QuickAccessPlugin instances.
getRawPixels() - Method in interface org.micromanager.data.Image: Returns the internal pixel data of this image.
getRawPixelsCopy() - Method in interface org.micromanager.data.Image: Returns a copy of the raw pixel data that getRawPixels returns.
getRawPixelsForComponent(int) - Method in interface org.micromanager.data.Image: Return a copy of the raw pixel data for the specified component.
getReceivedTime() - Method in interface org.micromanager.data.Metadata: The time at which the Java layer of Micro-Manager receives the image from the Core, expressed as a date-time string.
getRectangle(String, Rectangle) - Method in interface org.micromanager.PropertyMap
getRectangle(String, Rectangle) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getRectangleList(String, Rectangle...) - Method in interface org.micromanager.PropertyMap
getRectangleList(String, Iterable<Rectangle>) - Method in interface org.micromanager.PropertyMap
getRectangleList(String, Rectangle...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getRectangleList(String, Iterable<Rectangle>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getROI() - Method in interface org.micromanager.data.Metadata: The ROI of the camera when acquiring this image.
getSafeChannelName(int) - Method in interface org.micromanager.data.SummaryMetadata: Retrieve the name of the specified channel.
getSafeContrastGamma(int, Double) - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
getSafeContrastGamma(int, int, Double) - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
getSafeContrastMax(int, Integer) - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
getSafeContrastMax(int, int, Integer) - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
getSafeContrastMin(int, Integer) - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
getSafeContrastMin(int, int, Integer) - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
getSafeContrastSettings(int, DisplaySettings.ContrastSettings) - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
getSafeIsVisible(int, Boolean) - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
getSavePath() - Method in interface org.micromanager.data.Datastore: Get the intended or actual path where the data will be stored.
getScalingGamma() - Method in interface org.micromanager.display.ComponentDisplaySettings
getScalingMaximum() - Method in interface org.micromanager.display.ComponentDisplaySettings
getScalingMinimum() - Method in interface org.micromanager.display.ComponentDisplaySettings
getScopeData() - Method in interface org.micromanager.data.Metadata: Any information provided by Micro-Manager or its device adapters that is relevant to this image.
getScriptController() - Method in interface org.micromanager.Studio: Provides access to some utility methods for use in the Beanshell scripting panel.
getSequenceSettings() - Method in interface org.micromanager.data.SummaryMetadata: Settings that define the Multi-Dimensional Acquisition specified by the user to acquire this data set.
getSettings() - Method in interface org.micromanager.acquisition.AcquisitionSequenceStartedEvent: Return the SequenceSettings used to control the parameters of the acquisition.
getSettings() - Method in interface org.micromanager.data.ProcessorConfigurator: Provide a PropertyMap fully encapsulating the settings needed to set up a new DataProcessor.
getSettings(Class<?>) - Method in interface org.micromanager.UserProfile: Get an interface to save and retrieve settings.
getShort(String, short) - Method in interface org.micromanager.PropertyMap
getShort(String, short) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getShortList(String, short...) - Method in interface org.micromanager.PropertyMap
getShortList(String, Iterable<Short>) - Method in interface org.micromanager.PropertyMap
getShortList(String, short...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getShortList(String, Iterable<Short>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getShouldSyncChannels() - Method in interface org.micromanager.display.DisplaySettings: Deprecated.
getShutter() - Method in interface org.micromanager.events.ShutterEvent: Returns state of the shutter (true if shutter is open, false otherwise).
getShutter() - Method in interface org.micromanager.ShutterManager: Return whether or not the shutter is currently open.
getShutterDevices() - Method in interface org.micromanager.ShutterManager: Return a list of device names of devices that can be used as shutter devices.
getShutterManager() - Method in interface org.micromanager.Studio: Provides access to the ShutterManager for controlling the shutter state.
getSize() - Method in class org.micromanager.quickaccess.WidgetPlugin: Return the dimensionality of the widget, in cells.
getSkin() - Method in interface org.micromanager.ApplicationSkin: Returns the current Micro-Manager skin.
getSkinMode() - Method in interface org.micromanager.events.ApplicationSkinEvent: Returns the newly applied skin mode.
getSnapLiveManager() - Method in interface org.micromanager.Studio: Provides access to the Snap/Live display and associated logic.
getSource() - Method in interface org.micromanager.acquisition.AcquisitionEndedEvent: Return an Object used to identify the entity in charge of the acquisition.
getSource() - Method in interface org.micromanager.acquisition.AcquisitionStartedEvent: Return an Object used to identify the entity in charge of the acquisition.
getSplashImage() - Method in interface org.micromanager.IntroPlugin: Provide a "splash" image to display at the top of the intro dialog.
getStageDeviceLabel() - Method in class org.micromanager.StagePosition
getStagePosition() - Method in interface org.micromanager.data.Coords: Get the stage position index.
getStagePositionList() - Method in interface org.micromanager.data.SummaryMetadata: The stage positions that were to be visited in the acquisition.
getStagePositions() - Method in interface org.micromanager.data.SummaryMetadata: Deprecated.
- Use getStagePositionList() instead
getStandardDisplaySettings() - Method in interface org.micromanager.display.DisplayManager: Retrieve a DisplaySettings holding the values the user has saved as their default values.
getStartDate() - Method in interface org.micromanager.data.SummaryMetadata: The date and time at which the acquisition started.
getStdDev() - Method in class org.micromanager.display.HistogramData: Deprecated.

Retrieve the standard deviation of all samples in the dataset, or -1 if standard deviation calculation was disabled or if a calculation error occurred while calculating the standard deviation.
getStore() - Method in interface org.micromanager.acquisition.AcquisitionEndedEvent: Return the Datastore into which images were placed during the acquisition.
getString(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getString(String, String) - Method in interface org.micromanager.PropertyMap
getString(String, String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getString(Class<?>, String, String) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getString(key, fallback) instead
getStringArray(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
getStringArray(String, String[]) - Method in interface org.micromanager.PropertyMap: Deprecated.
getStringArray(Class<?>, String, String[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).getStringList(key, fallback) instead
getStringAsEnum(String, Class<E>, E) - Method in interface org.micromanager.PropertyMap: Get a string value, converted to an enum value.
getStringAsEnum(String, Class<E>, E) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getStringList(String, String...) - Method in interface org.micromanager.PropertyMap
getStringList(String, Iterable<String>) - Method in interface org.micromanager.PropertyMap
getStringList(String, String...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getStringList(String, Iterable<String>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getStringListAsEnumList(String, Class<E>, E...) - Method in interface org.micromanager.PropertyMap
getStringListAsEnumList(String, Class<E>, Iterable<E>) - Method in interface org.micromanager.PropertyMap: Get a collection of strings, converted to a collection of enum values.
getStringListAsEnumList(String, Class<E>, E...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getStringListAsEnumList(String, Class<E>, Iterable<E>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getSubMenu() - Method in interface org.micromanager.display.DisplayGearMenuPlugin: Indicate which sub-menu of the gear menu this plugin should appear in.
getSubMenu() - Method in interface org.micromanager.MenuPlugin: Indicate which sub-menu of the Plugins menu this plugin should appear in.
getSummaryMetadata() - Method in interface org.micromanager.data.DataProvider: Returns Summary Metadata.
getSummaryMetadata() - Method in interface org.micromanager.data.DataProviderHasNewSummaryMetadataEvent: Returns Summary Metadata.
getSummaryMetadata() - Method in interface org.micromanager.data.ProcessorContext: Access the SummaryMetadata of the Datastore that images will ultimately be inserted into.
getSummaryMetadata() - Method in interface org.micromanager.data.Storage: Retrieve the SummaryMetadata associated with this dataset.
getSummaryMetadataBuilder() - Method in interface org.micromanager.data.DataManager: Deprecated.
Use DataManager.summaryMetadataBuilder() instead
getT() - Method in interface org.micromanager.data.Coords: Shorthand for getTimePoint.
getTag() - Method in interface org.micromanager.data.Annotation: Return this annotation's tag.
getText() - Method in interface org.micromanager.alerts.UpdatableAlert: Returns the current text of the alert.
getTime() - Method in interface org.micromanager.data.Coords: Deprecated.
Due to looking like the physical time rather than an index. Use getTmePoint
getTimePoint() - Method in interface org.micromanager.data.Coords: Get the time point (frame) index.
getTitle() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
getTitle() - Method in interface org.micromanager.display.inspector.InspectorPanelController
getTitle() - Method in interface org.micromanager.display.overlay.Overlay: Return a human-readable name for this overlay.
getTitle() - Method in class org.micromanager.quickaccess.SimpleButtonPlugin: Returns the text to show in the button.
getUniqueSaveDirectory(String) - Method in interface org.micromanager.data.DataManager: Given a path string, create a unique string with that name.
getUnorderedImageCoords() - Method in interface org.micromanager.data.DataProvider
getUnorderedImageCoords() - Method in interface org.micromanager.data.Storage: Return an Iterable that provides access to all image coordinates in the Storage, in arbitrary order.
getUserData() - Method in interface org.micromanager.data.Metadata: Arbitrary additional metadata added by third-party code.
getUserData() - Method in interface org.micromanager.data.SummaryMetadata: Any general-purpose user meta data.
getUserName() - Method in interface org.micromanager.data.SummaryMetadata: The signed-in user of the machine that collected this data.
getUserProfile() - Method in interface org.micromanager.Studio: Provides access to the UserProfile instance for accessing per-user profiles.
getUUID() - Method in interface org.micromanager.data.Metadata: A unique identifier for this specific image.
getUUID(String, UUID) - Method in interface org.micromanager.PropertyMap
getUUID(String, UUID) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getUUIDList(String, UUID...) - Method in interface org.micromanager.PropertyMap
getUUIDList(String, Iterable<UUID>) - Method in interface org.micromanager.PropertyMap
getUUIDList(String, UUID...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getUUIDList(String, Iterable<UUID>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getValue() - Method in interface org.micromanager.events.PropertyChangedEvent: New value of the property.
getValueAsString(String, String) - Method in interface org.micromanager.PropertyMap
getValueAsString(String, String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
getValueType() - Method in interface org.micromanager.PropertyMap.OpaqueValue: Returns the type of the value.
getValueTypeForKey(String) - Method in interface org.micromanager.PropertyMap: Return a class indicating the type of the value for the given key.
getValueTypeForKey(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView: Return a class indicating the type of the value for the given key.
getVerbose() - Method in class org.micromanager.StagePosition: Verbose description of this StagePosition.
getVerboseStatus() - Method in interface org.micromanager.AutofocusPlugin: Returns a detailed status of the autofocus plugin/device.
getVersion() - Method in class org.micromanager.acquisition.SequenceSettings
getVersion() - Method in interface org.micromanager.CompatibilityInterface: Return the version of the running instance of Micro-Manager.
getVersion() - Method in interface org.micromanager.MMPlugin: Provide a version string.
getWaitInterval() - Method in interface org.micromanager.data.SummaryMetadata: Amount of time to wait between timepoints.
getWidth() - Method in interface org.micromanager.data.Image: Get the width of this image in pixels.
getWindow() - Method in interface org.micromanager.display.DisplayWindow: Get the java.awt.Window used for this image display.
getX() - Method in class org.micromanager.MultiStagePosition: Returns "X" coordinate of the position.
getXPos() - Method in interface org.micromanager.events.XYStagePositionChangedEvent: New X position of the stage in microns.
getXPositionUm() - Method in interface org.micromanager.data.Metadata: The X stage position of the sample for this image.
getY() - Method in class org.micromanager.MultiStagePosition: Returns "Y" coordinate of the position.
getYPos() - Method in interface org.micromanager.events.XYStagePositionChangedEvent: New Y position of the stage in microns.
getYPositionUm() - Method in interface org.micromanager.data.Metadata: The Y stage position of the sample for this image.
getZ() - Method in interface org.micromanager.data.Coords: Shorthand for getZSlice.
getZ() - Method in class org.micromanager.MultiStagePosition: Returns "Z" - focus coordinate of the position.
getZoom() - Method in interface org.micromanager.display.DisplayWindow: Get the current zoom ratio of the display.
getZoomRatio() - Method in interface org.micromanager.display.DisplaySettings: Zoom level expressed as a ratio (i.e.
getZPositionUm() - Method in interface org.micromanager.data.Metadata: The Z stage position of the sample for this image.
getZSlice() - Method in interface org.micromanager.data.Coords: Get the Z slice index.
getZStepUm() - Method in interface org.micromanager.data.SummaryMetadata: Distance between slices in a volume of data, in microns.
goToPosition(MultiStagePosition, CMMCore) - Static method in class org.micromanager.MultiStagePosition: Moves all stages to the specified positions.
groupName(String) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
GUIRefreshEvent - Interface in org.micromanager.events: This event posts whenever the GUI refreshes its state from the Core (e.g.

H

halt() - Method in interface org.micromanager.data.Pipeline: Halt image processing, so that the Pipeline will not produce any more images.
haltAcquisition() - Method in interface org.micromanager.acquisition.AcquisitionManager: Halt any ongoing acquisition as soon as possible, prompting users with a dialog for confirmation.
handleDisplayPosition(Coords) - Method in class org.micromanager.display.AbstractDataViewer
handleDisplaySettings(DisplaySettings) - Method in class org.micromanager.display.AbstractDataViewer: Arrange to apply new display settings.
hasAnnotation(String) - Method in interface org.micromanager.data.Datastore: Return whether an annotation with the given tag exists.
hasAxis(String) - Method in interface org.micromanager.data.Coords: Returns whether this coords has the given axis.
hasC() - Method in interface org.micromanager.data.Coords
hasChannelAxis() - Method in interface org.micromanager.data.Coords
hasElapsedTimeMs() - Method in interface org.micromanager.data.Metadata: Whether or not this image has metadata indicating the time elapsed since the start of the acquisition.
hashCode() - Method in class org.micromanager.MultiStagePosition
hashCode() - Method in class org.micromanager.StagePosition
hasImage(Coords) - Method in interface org.micromanager.data.DataProvider
hasImage(Coords) - Method in interface org.micromanager.data.Storage: Returns whether or not an image exists at the specified coordinates.
hasNext() - Method in class org.micromanager.PositionList.PosListIterator
hasP() - Method in interface org.micromanager.data.Coords
hasPositionName() - Method in interface org.micromanager.data.Metadata
hasProperty(String) - Method in class org.micromanager.MultiStagePosition: Checks if the position has a particular property.
hasStagePositionAxis() - Method in interface org.micromanager.data.Coords
hasT() - Method in interface org.micromanager.data.Coords
hasTimePointAxis() - Method in interface org.micromanager.data.Coords
hasZ() - Method in interface org.micromanager.data.Coords
hasZSliceAxis() - Method in interface org.micromanager.data.Coords
hide() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
HistogramData - Class in org.micromanager.display: Deprecated.
an improved API will be provided soon
HistogramData(int[], int, int, int, int, int, int, double, int, int) - Constructor for class org.micromanager.display.HistogramData: Deprecated.

Deprecated Histogram constructor.
histogramLogarithmic(boolean) - Method in interface org.micromanager.display.DisplaySettings.Builder: Whether the histogram should be shown with a logarithmic (true) or linear (false) y-axis.
histoRangeBits(int) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder

I

ij() - Method in interface org.micromanager.data.DataManager: Provide access to the ImageJConverter() object.
Image - Interface in org.micromanager.data: A 2-dimensional pixel plane with associated multi-dimensional coordinates and metadata.
ImageDeletedEvent - Interface in org.micromanager.data: This class signifies that an image has been deleted in the Datastore.
ImageExporter - Interface in org.micromanager.display: ImageExporters are used to generate linear sequences of images-as-rendered by a DisplayWindow.
ImageExporter.OutputFormat - Enum in org.micromanager.display: Allowed export formats.
imageHeight(Integer) - Method in interface org.micromanager.data.SummaryMetadata.Builder
ImageJConverter - Interface in org.micromanager.data: This class provides access to utility methods for interoperating with ImageJ.
imageNumber(Long) - Method in interface org.micromanager.data.Metadata.Builder
imageNumber(Long) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
ImageOverwrittenEvent - Interface in org.micromanager.data: This class signifies that an image has been overwritten in the Datastore.
IMAGES_DIFFER_IN_SIZE - Static variable in exception org.micromanager.data.ImagesDifferInSizeException
ImagesDifferInSizeException - Exception in org.micromanager.data: An unchecked exception thrown when an image is put into a datastore that already has an image of a different size and that does not support images differing in size (currently non of the MM Datastores support images differing in size.
ImagesDifferInSizeException() - Constructor for exception org.micromanager.data.ImagesDifferInSizeException
imageWidth(Integer) - Method in interface org.micromanager.data.SummaryMetadata.Builder
incrementalFocus() - Method in interface org.micromanager.AutofocusPlugin: Runs a single, incremental focusing step.
index(String, int) - Method in interface org.micromanager.data.Coords.Builder: Set the index along a given axis.
index(String, int) - Method in interface org.micromanager.data.Coords.CoordsBuilder
initialize() - Method in interface org.micromanager.AutofocusManager: Initializes all known autofocus plugins.
initialize() - Method in interface org.micromanager.AutofocusPlugin: Initializes the plugin.
initiallyExpand() - Method in interface org.micromanager.display.inspector.InspectorPanelController
insertImage(Image) - Method in interface org.micromanager.data.Pipeline: Insert an Image into the Pipeline.
insertSummaryMetadata(SummaryMetadata) - Method in interface org.micromanager.data.Pipeline: Pass a SummaryMetadata through the Pipeline to be modified by the Processors in it.
InspectorPanelController - Interface in org.micromanager.display.inspector
inspectorPanelDidChangeHeight(InspectorPanelController) - Method in interface org.micromanager.display.inspector.InspectorPanelListener: Must be called after changing minimum, preferred, and/or maximum height of the panel.
inspectorPanelDidChangeTitle(InspectorPanelController) - Method in interface org.micromanager.display.inspector.InspectorPanelListener: Must be called when the title of the inspector panel has changed.
InspectorPanelListener - Interface in org.micromanager.display.inspector
InspectorPanelPlugin - Interface in org.micromanager.display.inspector: A plugin providing a panel in the Inspector window.
inspectorPanelWillChangeHeight(InspectorPanelController) - Method in interface org.micromanager.display.inspector.InspectorPanelListener: Must be called before changing minimum, preferred, and/or maximum height of the panel.
intendedDimensions(Coords) - Method in interface org.micromanager.data.SummaryMetadata.Builder
intendedDimensions(Coords) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
intervalMs(double) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
intervalMs - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and intervalMs() instead
intervalMs() - Method in class org.micromanager.acquisition.SequenceSettings: Desired interval between the start of two consecutive time points in milliseconds.
IntroPlugin - Interface in org.micromanager: IntroPlugins are used to customize the intro dialog that prompts the user for which config file and profile to use.
is1DStagePosition() - Method in class org.micromanager.StagePosition
is2DStagePosition() - Method in class org.micromanager.StagePosition
isAcquisitionRunning() - Method in interface org.micromanager.acquisition.AcquisitionManager: Returns true when an acquisition is currently running (note: this function will not return true if live mode, snap, or "Camera --> Album" is currently running.
isApplicableToDataViewer(DataViewer) - Method in interface org.micromanager.display.inspector.InspectorPanelPlugin: Tell whether the InspectorPanel provided by this plugin is applicable to a given DataViewer.
isApplicationPipelineStepEnabled(int) - Method in interface org.micromanager.data.DataManager: Checks whether or not the plugin at position `index` in the list is enabled for the application pipeline.
isAutoscaleIgnoringZeros() - Method in interface org.micromanager.display.DisplaySettings: When autoscaling, take zero values into account or not? This can be useful for images that contain artificial zero values.
isAutostretchEnabled() - Method in interface org.micromanager.display.DisplaySettings: Whether to continuously apply autoscale.
isCanceled() - Method in interface org.micromanager.events.ShutdownCommencingEvent: Return whether or not shutdown has been canceled.
isChannelVisible(int) - Method in interface org.micromanager.display.DisplaySettings
isClosed() - Method in interface org.micromanager.display.DataViewer: Return true if this viewer has been closed.
isContinuousFocusEnabled() - Method in interface org.micromanager.AutofocusPlugin: Returns true if continuous autofocus has been enabled.
isContinuousFocusLocked() - Method in interface org.micromanager.AutofocusPlugin: Returns true if continuous autofocus is currently locked (successfully following the specimen).
isEmpty() - Method in interface org.micromanager.PropertyMap
isEmpty() - Method in interface org.micromanager.propertymap.MutablePropertyMapView: Return whether this view is empty.
isFrozen() - Method in interface org.micromanager.data.DataProvider: A dataProvider is frozen when no more images can be added.
isFullScreen() - Method in interface org.micromanager.display.DisplayWindow: Tell whether full screen mode is currently enabled.
isHalted() - Method in interface org.micromanager.data.Pipeline: Returns true if the pipeline has been halted (that is, its halt() method has been executed to completion), false otherwise.
isHistogramLogarithmic() - Method in interface org.micromanager.display.DisplaySettings: Whether the y-axis of the histogram uses a logarithmic or linear scale.
isLabelUnique(String) - Method in class org.micromanager.PositionList: Verify that the new label is unique.
isLiveModeOn() - Method in interface org.micromanager.SnapLiveManager: Returns whether live mode is on.
isLivePipelineStepEnabled(int) - Method in interface org.micromanager.data.DataManager: Checks whether or not the plugin at position `index` in the list is enabled for the live pipeline.
isMainExposureTime() - Method in interface org.micromanager.events.ChannelExposureEvent: Returns true if this channel is the currently-active channel (i.e.
isManaged(DataProvider) - Method in interface org.micromanager.display.DisplayManager: Returns true if the DataProvider is being managed by MicroManager.
isOn() - Method in interface org.micromanager.events.LiveModeEvent: Informs the caller if live mode is on or off.
isOurAcquisition(Object) - Method in interface org.micromanager.acquisition.AcquisitionManager: Test the provided Object, and return true if it corresponds to the "source" object that Micro-Manager's acquisition system uses when publishing AcquisitionStartedEvent and AcquisitionEndedEvent.
isPaused() - Method in interface org.micromanager.acquisition.AcquisitionManager: Returns true if the acquisition is currently paused.
isROIAutoscaleEnabled() - Method in interface org.micromanager.display.DisplaySettings: Whether to only look at the ROI when autoscaling.
isSynchronous() - Method in interface org.micromanager.data.Pipeline: Return whether the Pipeline is operating in synchronous or asynchronous modes.
isUniformChannelScalingEnabled() - Method in interface org.micromanager.display.DisplaySettings: Whether to use the same intensity scaling for every channel.
isUniformComponentScalingEnabled() - Method in interface org.micromanager.display.ChannelDisplaySettings
isUsable() - Method in interface org.micromanager.alerts.Alert: Returns whether or not this Alert is still visible to the user and can therefore be updated or have more content added to it.
isVerticallyResizableByUser() - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController: Indicate whether the panel can be resized vertically by the user.
isVerticallyResizableByUser() - Method in interface org.micromanager.display.inspector.InspectorPanelController
isVisible() - Method in interface org.micromanager.display.ChannelDisplaySettings: Indicates whether this is visible.
isVisible() - Method in interface org.micromanager.display.DataViewer: Return true if this viewer is visible.
isVisible() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings: Deprecated.
Use isVisible
isVisible() - Method in class org.micromanager.display.overlay.AbstractOverlay: Return whether this overlay is shown.
isVisible() - Method in interface org.micromanager.display.overlay.Overlay: Return whether this overlay is shown.
iterator() - Method in class org.micromanager.PositionList

K

keepShutterOpenChannels(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
keepShutterOpenChannels - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and keepShutterOpenChannels() instead
keepShutterOpenChannels() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to keep shutter open during channel changes.
keepShutterOpenChannels(Boolean) - Method in interface org.micromanager.data.SummaryMetadata.Builder
keepShutterOpenChannels(Boolean) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
keepShutterOpenSlices(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
keepShutterOpenSlices - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and keepShutterOpenSlices() instead
keepShutterOpenSlices() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to keep shutter open during z-stack stage movements.
keepShutterOpenSlices(Boolean) - Method in interface org.micromanager.data.SummaryMetadata.Builder
keepShutterOpenSlices(Boolean) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
keySet() - Method in interface org.micromanager.PropertyMap: Return an unmodifiable set containing all of the keys.
keySet() - Method in interface org.micromanager.propertymap.MutablePropertyMapView: Return a set view of all of the keys in this view.

L

live() - Method in interface org.micromanager.Studio: Provides access to the Snap/Live display and associated logic.
LiveModeEvent - Interface in org.micromanager.events: This class signals that live mode has been turned on or off.
load(File) - Method in class org.micromanager.PositionList: Load position list from a file.
load(String) - Method in class org.micromanager.PositionList: Load position list from a file.
loadAcquisition(String) - Method in interface org.micromanager.acquisition.AcquisitionManager: Load a file containing a SequenceSettings object, and apply the settings found in it to the Multi-D Acquisition (MDA) dialog.
loadData(String, boolean) - Method in interface org.micromanager.data.DataManager: Load the image data at the specified location on disk, and return a Datastore for that data.
loadData(Component, String, boolean) - Method in interface org.micromanager.data.DataManager: Load the image data at the specified location on disk, and return a Datastore for that data.
loadDisplays(Datastore) - Method in interface org.micromanager.display.DisplayManager: Load saved DisplayWindows for the given Datastore, which is assumed to represent data that is saved on disk.
loadJSON(File) - Method in interface org.micromanager.PropertyManager: Create a property map from its JSON-serialized form stored in a file.
loadJSON(File) - Static method in class org.micromanager.PropertyMaps: Create a property map from its JSON-serialized form stored in a file.
loadPropertyMap(String) - Method in interface org.micromanager.data.DataManager: Deprecated.
use PropertyMaps.loadJSON(File) instead
loadSequenceSettings(String) - Method in interface org.micromanager.acquisition.AcquisitionManager: Load a SequenceSettings file and return the SequenceSettings object.
loadSettingsFromFile(File) - Method in interface org.micromanager.quickaccess.QuickAccessManager: Load a settings file as generated by saveSettingsToFile().
logDebugMessage(String) - Method in interface org.micromanager.LogManager: Log a message to the core log, only if debug logging is currently enabled.
logError(Exception, String) - Method in interface org.micromanager.LogManager: Writes the stacktrace and a message to the Micro-Manager log (Corelog.txt).
logError(Exception) - Method in interface org.micromanager.LogManager: Writes a stacktrace to the Micro-Manager log.
logError(String) - Method in interface org.micromanager.LogManager: Writes an error to the Micro-Manager log (same as logMessage).
LogManager - Interface in org.micromanager: Provides access to logging and message display routines.
logMessage(String) - Method in interface org.micromanager.LogManager: Adds a message to the Micro-Manager log (found in Corelogtxt).
logs() - Method in interface org.micromanager.Studio: Provides access to Micro-Manager's logging functions, like logError(), showMessage(), etc.
loop(String, int, int) - Method in interface org.micromanager.display.ImageExporter: Add a new "inner loop" to the export parameters.

M

magnification(Double) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
makeActive() - Method in interface org.micromanager.Application: Move the main Micro-Manager window to the top of the user interface.
makeControls(DisplayWindow) - Method in interface org.micromanager.display.DisplayWindowControlsFactory
manage(DataProvider) - Method in interface org.micromanager.display.DisplayManager: Request that MicroManager manage the specified DataProvider for you.
markCurrentPosition() - Method in interface org.micromanager.PositionListManager: Deprecated.
since this function completely depends on the PositionListDlg.
matches(Coords) - Method in interface org.micromanager.data.Coords: Deprecated.
Use equality (after removing specific axes) instead
MenuPlugin - Interface in org.micromanager: A MenuPlugin is a plugin that should appear under the "Plugins" menu.
merge(PropertyMap) - Method in interface org.micromanager.PropertyMap: Deprecated.
message(String) - Method in interface org.micromanager.ScriptController: Displays text in the scripting console output window.
Metadata - Interface in org.micromanager.data: This interface defines the metadata for Images.
Metadata.Builder - Interface in org.micromanager.data: Builder for Metadata.
Metadata.MetadataBuilder - Interface in org.micromanager.data: Deprecated.
Use Metadata.Builder instead
metadataBuilder() - Method in interface org.micromanager.data.DataManager: Generate a "blank" MetadataBuilder for use in constructing new Metadata instances.
migrate(PropertyMap, MutablePropertyMapView) - Method in interface org.micromanager.profile.UserProfileMigration: Perform a migration from old settings storage.
MMEvent - Interface in org.micromanager: Interface that all events in Micro-Manager should inherit from.
MMGenericPlugin - Interface in org.micromanager: Micro-Manager plugin interface.
MMPlugin - Interface in org.micromanager: This interface is the base interface for all Micro-Manager plugins.
MultiStagePosition - Class in org.micromanager: Definition of a position in space in terms of available stages/drives.
MultiStagePosition() - Constructor for class org.micromanager.MultiStagePosition: Default constructor.
MultiStagePosition(String, double, double, String, double) - Constructor for class org.micromanager.MultiStagePosition: Convenient constructor where the motion system consists of one XY stage and one focus stage.
MutablePropertyMapView - Interface in org.micromanager.propertymap: An interface to a property-map-like object that can be modified.

N

name(String) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
name() - Method in interface org.micromanager.profile.UserProfileMigration: The current (modern) key under which the relevant setting is stored.
newInstance(MultiStagePosition) - Static method in class org.micromanager.MultiStagePosition: Copy constructor.
newInstance(PositionList) - Static method in class org.micromanager.PositionList: This looks like a static copy constructor.
newInstance(StagePosition) - Static method in class org.micromanager.StagePosition: Creates a copy of a StagePosition object.
NewPipelineEvent - Interface in org.micromanager.data: This class signifies that the configuration of the application pipeline has changed, giving entities that use that pipeline an opportunity to make a new copy of it (by invoking DataManager.copyApplicationPipeline()).
NewPositionListEvent - Interface in org.micromanager.events: This event posts when the application's Stage Position List changes (positions added, removed, or moved).
next() - Method in class org.micromanager.PositionList.PosListIterator
notifyChangeListeners() - Method in class org.micromanager.PositionList: Notifies all changeListeners to the list that something changed.
notifyPipelineChanged() - Method in interface org.micromanager.data.DataManager: Notify the application that the state of one of the processors in the pipeline has changed, and thus that entities that use the application pipeline should grab a new copy of it.
numAxes - Variable in class org.micromanager.StagePosition: Deprecated.
Use StagePosition.set1DPosition(java.lang.String, double) or StagePosition.set2DPosition(java.lang.String, double, double) to set; use StagePosition.getNumberOfStageAxes(), StagePosition.is1DStagePosition(), or StagePosition.is2DStagePosition() to access.
numFrames(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
numFrames - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and numFrames() instead
numFrames() - Method in class org.micromanager.acquisition.SequenceSettings: Number of time points to be acquired.

O

offset(String, int) - Method in interface org.micromanager.data.Coords.Builder: Offset the given axis by a given count.
offset(String, int) - Method in interface org.micromanager.data.Coords.CoordsBuilder
onPluginSelected(DisplayWindow) - Method in interface org.micromanager.display.DisplayGearMenuPlugin: This method will be called when the plugin is selected from the gear menu.
onPluginSelected() - Method in interface org.micromanager.MenuPlugin: This method will be called when the plugin is selected from the PluginsMenu.
org.micromanager - package org.micromanager: MMStudio application and Java API.
org.micromanager.acquisition - package org.micromanager.acquisition: This package contains classes for acquiring data and accessing Micro- Manager's Acquisition Engine.
org.micromanager.alerts - package org.micromanager.alerts
org.micromanager.data - package org.micromanager.data: This package contains classes related to the storage and internal representation of image data and metadata.
org.micromanager.display - package org.micromanager.display: This package contains classes related to Micro-Manager's display windows, which are used to show image data and metadata to the user.
org.micromanager.display.inspector - package org.micromanager.display.inspector
org.micromanager.display.overlay - package org.micromanager.display.overlay
org.micromanager.events - package org.micromanager.events: This package contains events that can be subscribed to via the EventManager.registerForEvents() method.
org.micromanager.profile - package org.micromanager.profile
org.micromanager.propertymap - package org.micromanager.propertymap
org.micromanager.quickaccess - package org.micromanager.quickaccess: This package contains classes related to Micro-Manager's Quick-Access Window, which provides easy access to certain user-selected controls.
outputImage(Image) - Method in interface org.micromanager.data.ProcessorContext: Hand a newly-generated Image to the ProcessorContext.
Overlay - Interface in org.micromanager.display.overlay: A graphic object displayed over images.
overlayConfigurationChanged(Overlay) - Method in interface org.micromanager.display.overlay.OverlayListener: Called by the overlay when a repaint is required.
OverlayListener - Interface in org.micromanager.display.overlay
OverlayPlugin - Interface in org.micromanager.display.overlay: A plugin providing overlays.
overlayTitleChanged(Overlay) - Method in interface org.micromanager.display.overlay.OverlayListener: Called by the overlay when its title has changed.
overlayVisibleChanged(Overlay) - Method in interface org.micromanager.display.overlay.OverlayListener: Called by the overlay when it is shown or hidden.

P

p(int) - Method in interface org.micromanager.data.Coords.Builder: Shorthand for stagePosition.
P - Static variable in interface org.micromanager.data.Coords: Axis label for the stage position axis (short form).
paintOverlay(Graphics2D, Rectangle, DisplaySettings, List<Image>, Image, Rectangle2D.Float) - Method in class org.micromanager.display.overlay.AbstractOverlay: Paint the overlay to the given graphics context.
paintOverlay(Graphics2D, Rectangle, DisplaySettings, List<Image>, Image, Rectangle2D.Float) - Method in interface org.micromanager.display.overlay.Overlay: Paint the overlay to the given graphics context.
Pipeline - Interface in org.micromanager.data: Pipelines are used to apply a sequence of Processors to Images prior to those images being inserted into a Datastore.
PipelineErrorException - Exception in org.micromanager.data: This exception is thrown when Pipeline.insertImage() has been called after an error occurred in one of the Processors in the Pipeline.
PipelineErrorException() - Constructor for exception org.micromanager.data.PipelineErrorException
PipelineErrorException(String) - Constructor for exception org.micromanager.data.PipelineErrorException
pixelAspect(Double) - Method in interface org.micromanager.data.Metadata.Builder
pixelAspect(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
pixelSizeAffine(AffineTransform) - Method in interface org.micromanager.data.Metadata.Builder
pixelSizeAffine(AffineTransform) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
PixelSizeAffineChangedEvent - Interface in org.micromanager.events: This event posts when the affine transform, describing the relation between stage movement and camera coordinates, changes.
PixelSizeChangedEvent - Interface in org.micromanager.events: This event posts when the pixel size, the size of a camera pixel in the object plane, changes.
pixelSizeUm(Double) - Method in interface org.micromanager.data.Metadata.Builder
pixelSizeUm(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
playbackFPS(double) - Method in interface org.micromanager.display.DisplaySettings.Builder
PluginManager - Interface in org.micromanager: This class provides access to plugins that have been detected by Micro-Manager at startup.
plugins() - Method in interface org.micromanager.Studio: Provides access to the PluginManager for accessing plugin instances.
PositionList - Class in org.micromanager: Navigation list of positions for the Stages.
PositionList() - Constructor for class org.micromanager.PositionList: Constructor of navigation list of positions for the Stages.
PositionList.PosListIterator - Class in org.micromanager: Provides an iterator for a PositionList.
PositionListManager - Interface in org.micromanager: This entity provides access to methods for interacting with the Stage PositionList.
positionName(String) - Method in interface org.micromanager.data.Metadata.Builder
positionName(String) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
positions() - Method in interface org.micromanager.Studio: Provides access to the PositionListManager for interacting with the Stage Position List.
PosListIterator(PositionList) - Constructor for class org.micromanager.PositionList.PosListIterator
post(Object) - Method in interface org.micromanager.events.EventManager: Post an event on the EventBus, so that subscribers for that event can be notified.
postAlert(String, Class<?>, String) - Method in interface org.micromanager.alerts.AlertManager: Send notification of a specific event.
postCustomAlert(String, JComponent) - Method in interface org.micromanager.alerts.AlertManager: Create an alert containing the provided special contents.
postEvent(Object) - Method in class org.micromanager.display.AbstractDataViewer: Post an event on the viewer event bus.
postUpdatableAlert(String, String) - Method in interface org.micromanager.alerts.AlertManager: Create a UpdatableAlert.
prefix(String) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
prefix - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and prefix() instead
prefix() - Method in class org.micromanager.acquisition.SequenceSettings: Acquisition name.
prefix(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
prefix(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
processImage(Image, ProcessorContext) - Method in interface org.micromanager.data.Processor: Process an Image.
Processor - Interface in org.micromanager.data: Processors manipulate images before they are added to a Datastore.
ProcessorConfigurator - Interface in org.micromanager.data: ProcessorPluginConfigurators are used to generate the PropertyMaps needed to set up a ProcessorFactory.
ProcessorContext - Interface in org.micromanager.data: A ProcessorContext is an object that allows Processors to communicate with the ProcessorPipeline.
ProcessorFactory - Interface in org.micromanager.data: A ProcessorFactory is an object that generates new DataProcessors.
ProcessorPlugin - Interface in org.micromanager.data: A ProcessorPlugin is the "root" class for creating Processors, which are used to modify images as they are collected by Micro-Manager.
processSummaryMetadata(SummaryMetadata) - Method in interface org.micromanager.data.Processor: Update the SummaryMetadata of the Datastore that images will ultimately be stored in.
profile() - Method in interface org.micromanager.Studio: Provides access to the UserProfile instance for accessing per-user profiles.
profileName(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
profileName(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
promptForDataToLoad(Window, boolean) - Method in interface org.micromanager.data.DataManager: Display a dialog prompting the user to select a location on disk, and invoke loadData() on that selection.
promptToCloseWindows() - Method in interface org.micromanager.display.DisplayManager: Show a dialog to the user giving them a prompt to close all open windows, and allowing them to decide whether or not to be prompted to save each unsaved open window (or simply cancel the entire action).
promptToSave(Datastore, DisplayWindow) - Method in interface org.micromanager.display.DisplayManager: Display a prompt for the user to save their data.
properties() - Method in interface org.micromanager.Studio: Provides access to the PropertyManagerAPI.
PropertiesChangedEvent - Interface in org.micromanager.events: This class signals when any property of the microscope has changed.
PropertyChangedEvent - Interface in org.micromanager.events: This class provides information when a specific property changes.
PropertyManager - Interface in org.micromanager: Provides access to PropertyMaps.
PropertyMap - Interface in org.micromanager: An immutable typed key-value store for various settings.
PropertyMap.Builder - Interface in org.micromanager: Builder for PropertyMap.
PropertyMap.OpaqueValue - Interface in org.micromanager: A value that can be stored in a property map.
PropertyMap.PropertyMapBuilder - Interface in org.micromanager: Deprecated.
PropertyMap.TypeMismatchException - Exception in org.micromanager: Deprecated.
If necessary, catch ClassCastException instead.
propertyMapBuilder() - Method in interface org.micromanager.PropertyManager: Provides an easy way for a script to obtain a PropertyMap Builder.
PropertyMaps - Class in org.micromanager: Static methods to create PropertyMap instances.
putAffineTransform(String, AffineTransform) - Method in interface org.micromanager.PropertyMap.Builder
putAffineTransform(String, AffineTransform) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putAffineTransformList(String, AffineTransform...) - Method in interface org.micromanager.PropertyMap.Builder
putAffineTransformList(String, Iterable<AffineTransform>) - Method in interface org.micromanager.PropertyMap.Builder
putAffineTransformList(String, AffineTransform...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putAffineTransformList(String, Iterable<AffineTransform>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putAll(PropertyMap) - Method in interface org.micromanager.PropertyMap.Builder
putAll(PropertyMap) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putBoolean(String, Boolean) - Method in interface org.micromanager.PropertyMap.Builder
putBoolean(String, Boolean) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putBoolean(String, Boolean) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putBooleanArray(String, Boolean[]) - Method in interface org.micromanager.PropertyMap.Builder: Deprecated.
Use PropertyMap.Builder.putBooleanList(java.lang.String, boolean...) instead.
putBooleanArray(String, Boolean[]) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putBooleanList(String, boolean...) - Method in interface org.micromanager.PropertyMap.Builder
putBooleanList(String, Iterable<Boolean>) - Method in interface org.micromanager.PropertyMap.Builder
putBooleanList(String, boolean...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putBooleanList(String, Iterable<Boolean>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putByte(String, Byte) - Method in interface org.micromanager.PropertyMap.Builder
putByte(String, Byte) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putByteList(String, byte...) - Method in interface org.micromanager.PropertyMap.Builder
putByteList(String, Iterable<Byte>) - Method in interface org.micromanager.PropertyMap.Builder
putByteList(String, byte...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putByteList(String, Iterable<Byte>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putColor(String, Color) - Method in interface org.micromanager.PropertyMap.Builder
putColor(String, Color) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putColorList(String, Color...) - Method in interface org.micromanager.PropertyMap.Builder
putColorList(String, Iterable<Color>) - Method in interface org.micromanager.PropertyMap.Builder
putColorList(String, Color...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putColorList(String, Iterable<Color>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putDimension(String, Dimension) - Method in interface org.micromanager.PropertyMap.Builder
putDimension(String, Dimension) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putDimensionList(String, Dimension...) - Method in interface org.micromanager.PropertyMap.Builder
putDimensionList(String, Iterable<Dimension>) - Method in interface org.micromanager.PropertyMap.Builder
putDimensionList(String, Dimension...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putDimensionList(String, Iterable<Dimension>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putDouble(String, Double) - Method in interface org.micromanager.PropertyMap.Builder
putDouble(String, Double) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putDouble(String, Double) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putDoubleArray(String, Double[]) - Method in interface org.micromanager.PropertyMap.Builder: Deprecated.
Use PropertyMap.Builder.putDoubleList(java.lang.String, double...) instead.
putDoubleArray(String, Double[]) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putDoubleList(String, double...) - Method in interface org.micromanager.PropertyMap.Builder
putDoubleList(String, Iterable<Double>) - Method in interface org.micromanager.PropertyMap.Builder
putDoubleList(String, double...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putDoubleList(String, Iterable<Double>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putEnumAsString(String, E) - Method in interface org.micromanager.PropertyMap.Builder
putEnumAsString(String, E) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putEnumListAsStringList(String, E...) - Method in interface org.micromanager.PropertyMap.Builder
putEnumListAsStringList(String, Iterable<E>) - Method in interface org.micromanager.PropertyMap.Builder
putEnumListAsStringList(String, E...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putEnumListAsStringList(String, Iterable<E>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putFloat(String, Float) - Method in interface org.micromanager.PropertyMap.Builder
putFloat(String, Float) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putFloatList(String, float...) - Method in interface org.micromanager.PropertyMap.Builder
putFloatList(String, Iterable<Float>) - Method in interface org.micromanager.PropertyMap.Builder
putFloatList(String, float...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putFloatList(String, Iterable<Float>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putImage(Image) - Method in interface org.micromanager.data.Datastore: Insert an image into the Datastore.
putImage(Image) - Method in interface org.micromanager.data.RewritableDatastore: Insert an image into the Datastore.
putImage(Image) - Method in interface org.micromanager.data.Storage: Insert an Image into the Storage, so that it may be returned by later getImage() calls.
putInt(String, Integer) - Method in interface org.micromanager.PropertyMap.Builder: Deprecated.
Use PropertyMap.Builder.putInteger(java.lang.String, java.lang.Integer) instead.
putInt(String, Integer) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putIntArray(String, Integer[]) - Method in interface org.micromanager.PropertyMap.Builder: Deprecated.
Use PropertyMap.Builder.putIntegerList(java.lang.String, int...) instead.
putIntArray(String, Integer[]) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putInteger(String, Integer) - Method in interface org.micromanager.PropertyMap.Builder
putInteger(String, Integer) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putIntegerList(String, int...) - Method in interface org.micromanager.PropertyMap.Builder
putIntegerList(String, Iterable<Integer>) - Method in interface org.micromanager.PropertyMap.Builder
putIntegerList(String, int...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putIntegerList(String, Iterable<Integer>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putLong(String, Long) - Method in interface org.micromanager.PropertyMap.Builder
putLong(String, Long) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putLong(String, Long) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putLongArray(String, Long[]) - Method in interface org.micromanager.PropertyMap.Builder: Deprecated.
Use PropertyMap.Builder.putLongList(java.lang.String, long...) instead.
putLongArray(String, Long[]) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putLongList(String, long...) - Method in interface org.micromanager.PropertyMap.Builder
putLongList(String, Iterable<Long>) - Method in interface org.micromanager.PropertyMap.Builder
putLongList(String, long...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putLongList(String, Iterable<Long>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putOpaqueValue(String, PropertyMap.OpaqueValue) - Method in interface org.micromanager.PropertyMap.Builder
putPoint(String, Point) - Method in interface org.micromanager.PropertyMap.Builder
putPoint(String, Point) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putPointList(String, Point...) - Method in interface org.micromanager.PropertyMap.Builder
putPointList(String, Iterable<Point>) - Method in interface org.micromanager.PropertyMap.Builder
putPointList(String, Point...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putPointList(String, Iterable<Point>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putPropertyMap(String, PropertyMap) - Method in interface org.micromanager.PropertyMap.Builder
putPropertyMap(String, PropertyMap) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putPropertyMap(String, PropertyMap) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putPropertyMapList(String, PropertyMap...) - Method in interface org.micromanager.PropertyMap.Builder
putPropertyMapList(String, Iterable<PropertyMap>) - Method in interface org.micromanager.PropertyMap.Builder
putPropertyMapList(String, PropertyMap...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putPropertyMapList(String, Iterable<PropertyMap>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putRectangle(String, Rectangle) - Method in interface org.micromanager.PropertyMap.Builder
putRectangle(String, Rectangle) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putRectangleList(String, Rectangle...) - Method in interface org.micromanager.PropertyMap.Builder
putRectangleList(String, Iterable<Rectangle>) - Method in interface org.micromanager.PropertyMap.Builder
putRectangleList(String, Rectangle...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putRectangleList(String, Iterable<Rectangle>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putShort(String, Short) - Method in interface org.micromanager.PropertyMap.Builder
putShort(String, Short) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putShortList(String, short...) - Method in interface org.micromanager.PropertyMap.Builder
putShortList(String, Iterable<Short>) - Method in interface org.micromanager.PropertyMap.Builder
putShortList(String, short...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putShortList(String, Iterable<Short>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putString(String, String) - Method in interface org.micromanager.PropertyMap.Builder
putString(String, String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putString(String, String) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putStringArray(String, String[]) - Method in interface org.micromanager.PropertyMap.Builder: Deprecated.
Use PropertyMap.Builder.putStringList(java.lang.String, java.lang.String...) instead.
putStringArray(String, String[]) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder: Deprecated.
putStringList(String, String...) - Method in interface org.micromanager.PropertyMap.Builder
putStringList(String, Iterable<String>) - Method in interface org.micromanager.PropertyMap.Builder
putStringList(String, String...) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putStringList(String, Iterable<String>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
putUUID(String, UUID) - Method in interface org.micromanager.PropertyMap.Builder
putUUIDList(String, UUID...) - Method in interface org.micromanager.PropertyMap.Builder
putUUIDList(String, Iterable<UUID>) - Method in interface org.micromanager.PropertyMap.Builder

Q

quickAccess() - Method in interface org.micromanager.Studio: Provides access to the QuickAccessManager for accessing the Quick-Access Panel system.
QuickAccessManager - Interface in org.micromanager.quickaccess: The QuickAccessManager provides API access to the Quick Access Panel(s).
QuickAccessPlugin - Class in org.micromanager.quickaccess: QuickAccessPlugins are used for controls that can show up in the Quick- Access Window, which shows frequently-used controls.
QuickAccessPlugin() - Constructor for class org.micromanager.quickaccess.QuickAccessPlugin

R

receivedTime(String) - Method in interface org.micromanager.data.Metadata.Builder
receivedTime(String) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
refresh() - Method in interface org.micromanager.AutofocusManager: Update the list of available autofocus devices by scanning the system for autofocus device adapters and AutofocusPlugins.
refreshGUI() - Method in interface org.micromanager.Application: Updates the GUI so that its state reflects the current state of the hardware (as understood by the Micro-Manager Core).
refreshGUIFromCache() - Method in interface org.micromanager.Application: Updates the GUI so that its state reflects the current state of the hardware (as understood by the Micro-Manager Core).
registerForEvents(Object) - Method in interface org.micromanager.data.DataProvider
registerForEvents(Object) - Method in class org.micromanager.display.AbstractDataViewer
registerForEvents(Object) - Method in interface org.micromanager.display.DataViewer: Register an object to receive events on the viewer event bus.
registerForEvents(Object) - Method in interface org.micromanager.EventPublisher: Register an object to receive events on the viewer event bus.
registerForEvents(Object) - Method in interface org.micromanager.events.EventManager: Register the specified object to receive events.
registerMigrations(Class<?>, UserProfileMigration...) - Static method in class org.micromanager.profile.UserProfileMigrator
relativeZSlice(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
relativeZSlice - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and relativeZSlice() instead
relativeZSlice() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to base the z Top and Bottom for a z stack relative to a referent position or treat them as absolute values.
remove(StagePosition) - Method in class org.micromanager.MultiStagePosition: Removed one stage position point.
remove() - Method in class org.micromanager.PositionList.PosListIterator
remove(String) - Method in interface org.micromanager.PropertyMap.Builder
remove(String) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
removeAll(Collection<?>) - Method in interface org.micromanager.PropertyMap.Builder
removeAll(Collection<?>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
removeAxis(String) - Method in interface org.micromanager.data.Coords.Builder: Remove the specified axis.
removeAxis(String) - Method in interface org.micromanager.data.Coords.CoordsBuilder
removeChangeListener(ChangeListener) - Method in class org.micromanager.PositionList: Removes the given listener.
removeInspectorPanelListener(InspectorPanelListener) - Method in class org.micromanager.display.inspector.AbstractInspectorPanelController
removeInspectorPanelListener(InspectorPanelListener) - Method in interface org.micromanager.display.inspector.InspectorPanelController
removeListener(DataViewerListener) - Method in interface org.micromanager.display.DataViewer: No longer notify this listener.
removeOverlay(Overlay) - Method in interface org.micromanager.display.DisplayWindow: Remove a graphical overlay.
removeOverlayListener(OverlayListener) - Method in class org.micromanager.display.overlay.AbstractOverlay: Remove a listener.
removeOverlayListener(OverlayListener) - Method in interface org.micromanager.display.overlay.Overlay: Remove a listener.
removePosition(int) - Method in class org.micromanager.PositionList: Removes a specific position based on the index.
removeViewer(DataViewer) - Method in interface org.micromanager.display.DisplayManager: Cause Micro-Manager to stop tracking a DataViewer that was previously added with addViewer().
replacePosition(int, MultiStagePosition) - Method in class org.micromanager.PositionList: Replaces position in the list with the new position.
replaceWithPropertyMap(PropertyMap) - Method in class org.micromanager.PositionList: replaces the content of this PositionList with the content of the given PropertyMap.
requestToClose() - Method in interface org.micromanager.display.DisplayWindow: Close this display window, giving its owner a chance to cancel closing.
resetInterpreter() - Method in interface org.micromanager.ScriptController: Clears all methods and variables defined in the script interpreter.
resetLoops() - Method in interface org.micromanager.display.ImageExporter: Reset the current export loop parameters to empty.
resume() - Method in interface org.micromanager.ApplicationSkin: Restores the mode that was active before suspendToMode was called.
retainAll(Collection<?>) - Method in interface org.micromanager.PropertyMap.Builder
retainAll(Collection<?>) - Method in interface org.micromanager.propertymap.MutablePropertyMapView
RewritableDatastore - Interface in org.micromanager.data: RewritableDatastores are Datastores that allow images and SummaryMetadata to be deleted or overwritten after they have been inserted.
RewritableStorage - Interface in org.micromanager.data: This interface is for Storage entities that allow the overwriting and deletion of Images and SummaryMetadata, as per RewritableDatastore.
ROI(Rectangle) - Method in interface org.micromanager.data.Metadata.Builder: Same as Metadata.Builder.roi(java.awt.Rectangle).
roi(Rectangle) - Method in interface org.micromanager.data.Metadata.Builder
ROI(Rectangle) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
roiAutoscale(boolean) - Method in interface org.micromanager.display.DisplaySettings.Builder
root(String) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
root - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and root() instead
root() - Method in class org.micromanager.acquisition.SequenceSettings: Directory where data will be saved.
runAcquisition() - Method in interface org.micromanager.acquisition.AcquisitionManager: Executes Acquisition with settings as in the MDA dialog.
runAcquisition(String, String) - Method in interface org.micromanager.acquisition.AcquisitionManager: Executes Acquisition with current settings but allows for changing the data path.
runAcquisitionNonblocking() - Method in interface org.micromanager.acquisition.AcquisitionManager: As runAcquisition, but will return as soon as the acquisition is set up and started; useful for code that wants access to the Datastore for the acquisition before it finishes.
runAcquisitionWithSettings(SequenceSettings, boolean) - Method in interface org.micromanager.acquisition.AcquisitionManager: Execute an acquisition using the provided SequenceSettings.
runFile(File) - Method in interface org.micromanager.ScriptController: Execute the script located in the given file.

S

safeUpdateChannelColor(Color, int) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
safeUpdateContrastSettings(DisplaySettings.ContrastSettings, int) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
save(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
save - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and save() instead
save() - Method in class org.micromanager.acquisition.SequenceSettings: Whether the data acquisition should be stored on disk.
save() - Method in interface org.micromanager.data.Annotation: Commit the changes to this annotation to disk.
save(Component) - Method in interface org.micromanager.data.Datastore: Deprecated.
Use Datastore.save(Component, boolean) instead
save(Component, boolean) - Method in interface org.micromanager.data.Datastore: Saves the datastore to an interactively determined path.
save(Datastore.SaveMode, String) - Method in interface org.micromanager.data.Datastore: Saves the datastore to the given path using the given format (SaveMode) Will save synchronously (i.e.
save(Datastore.SaveMode, String, boolean) - Method in interface org.micromanager.data.Datastore: Saves the datastore to the given path using the given format (SaveMode).
save(File) - Method in class org.micromanager.PositionList: Save list to a file.
save(String) - Method in class org.micromanager.PositionList: Save list to a file.
save(String) - Method in interface org.micromanager.PropertyMap: Deprecated.
saveConfigPresets(String, boolean) - Method in interface org.micromanager.Application: Save the current state of the config file to the specified path.
saveJSON(File, boolean, boolean) - Method in interface org.micromanager.PropertyMap: Save to a file as JSON.
saveMode(Datastore.SaveMode) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
saveMode() - Method in class org.micromanager.acquisition.SequenceSettings: File format to be used to save this acquisition when SequenceSettings.save() is set.
saveSequenceSettings(SequenceSettings, String) - Method in interface org.micromanager.acquisition.AcquisitionManager: Save the provided SequenceSettings object to disk at the specified path.
saveSettings() - Method in interface org.micromanager.AutofocusPlugin: Stores settings.
saveSettingsToFile(File) - Method in interface org.micromanager.quickaccess.QuickAccessManager: Save the Quick Access Panel settings to a file, so they may be transferred between users or to another system.
scalingGamma(double) - Method in interface org.micromanager.display.ComponentDisplaySettings.Builder
scalingMaximum(long) - Method in interface org.micromanager.display.ComponentDisplaySettings.Builder
scalingMinimum(long) - Method in interface org.micromanager.display.ComponentDisplaySettings.Builder
scalingRange(long, long) - Method in interface org.micromanager.display.ComponentDisplaySettings.Builder
scopeData(PropertyMap) - Method in interface org.micromanager.data.Metadata.Builder: Add device property data.
scopeData(PropertyMap) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
ScriptController - Interface in org.micromanager: Provides access to some utility methods for use in the Beanshell scripting panel.
ScriptController.ScriptStoppedException - Exception in org.micromanager: This exception signifies that the Beanshell interpreter has a stop request pending, which prevents most interactions with the system.
scripter() - Method in interface org.micromanager.Studio: Provides access to some utility methods for use in the Beanshell scripting panel.
ScriptStoppedException(String) - Constructor for exception org.micromanager.ScriptController.ScriptStoppedException: Exception thrown when the interpreted has a stop request pending.
SequenceSettings - Class in org.micromanager.acquisition: SequenceSettings objects contain the parameters describing how to run a single acquisition.
sequenceSettings(SequenceSettings) - Method in interface org.micromanager.data.SummaryMetadata.Builder
SequenceSettings.Builder - Class in org.micromanager.acquisition: SequenceSettings Builder.
sequenceSettingsBuilder() - Method in interface org.micromanager.acquisition.AcquisitionManager: Provides an empty Sequence Settings Builder.
set1DPosition(String, double) - Method in class org.micromanager.StagePosition: Sets the position of a stage device in this StagePosition instance.
set2DPosition(String, double, double) - Method in class org.micromanager.StagePosition: Sets the position of an XY stage device in this StagePosition instance.
setAcquisitionSettings(SequenceSettings) - Method in interface org.micromanager.acquisition.AcquisitionManager: Apply new acquisition settings.
setApplicationPipeline(List<ProcessorPlugin>) - Method in interface org.micromanager.data.DataManager: Set the current application pipeline to be the provided list of ProcessorPlugins.
setApplicationPipelineStepEnabled(int, boolean) - Method in interface org.micromanager.data.DataManager: Sets whether or not the plugin at position `index` in the list is enabled for the application pipeline.
setAutofocusMethod(AutofocusPlugin) - Method in interface org.micromanager.AutofocusManager: Set the current AutofocusPlugin to use for performing autofocus actions.
setAutofocusMethodByName(String) - Method in interface org.micromanager.AutofocusManager: Set the current AutofocusPlugin by name.
setAutoShutter(boolean) - Method in interface org.micromanager.ShutterManager: Turn autoshutter on or off.
setBoolean(Class<?>, String, Boolean) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putBoolean(key, value) instead
setBooleanArray(Class<?>, String, Boolean[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putBooleanList(key, value) instead
setCameraTransform(AffineTransform, String) - Method in interface org.micromanager.CompatibilityInterface: Deprecated.
- Use core.setPixelSizeAffine(config, DoubleVector transform) instead
setChannelExposureTime(String, String, double) - Method in interface org.micromanager.Application: Updates the exposure time associated with the given preset.
setConfiguration(PropertyMap) - Method in class org.micromanager.display.overlay.AbstractOverlay: Configure the overlay with the given parameters.
setConfiguration(PropertyMap) - Method in interface org.micromanager.display.overlay.Overlay: Configure the overlay with the given parameters.
setContext(Studio) - Method in interface org.micromanager.MMPlugin: Receive the Studio object needed to make API calls.
setCustomTitle(String) - Method in interface org.micromanager.display.DisplayWindow: Add a custom extra string to the title of this display.
setDefaultXYStage(String) - Method in class org.micromanager.MultiStagePosition: Defines which stage serves as the default XY motion control device.
setDefaultZStage(String) - Method in class org.micromanager.MultiStagePosition: Defines which stage serves as focus control.
setDisplay(DisplayWindow) - Method in interface org.micromanager.display.ImageExporter: Set the display to use for image exporting.
setDisplayedImageTo(Coords) - Method in class org.micromanager.display.AbstractDataViewer: Deprecated.
user code should call setDisplayPosition
setDisplayedImageTo(Coords) - Method in interface org.micromanager.display.DataViewer: Deprecated.
use DataViewer.setDisplayPosition(Coords) instead
setDisplayPosition(Coords, boolean) - Method in class org.micromanager.display.AbstractDataViewer: Implements setDisplayPosition.
setDisplayPosition(Coords) - Method in class org.micromanager.display.AbstractDataViewer
setDisplayPosition(Coords, boolean) - Method in interface org.micromanager.display.DataViewer: Display the images at the specified coordinates in the data provider.
setDisplayPosition(Coords) - Method in interface org.micromanager.display.DataViewer: Display the images at the specified coordinates in the data provider.
setDisplaySettings(DisplaySettings) - Method in class org.micromanager.display.AbstractDataViewer: Implements setDisplaySettings.
setDisplaySettings(DisplaySettings) - Method in interface org.micromanager.display.DataViewer: Set the display settings.
setDouble(Class<?>, String, Double) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putDouble(key, value) instead
setDoubleArray(Class<?>, String, Double[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putDoubleList(key, value) instead
setExpanded(boolean) - Method in interface org.micromanager.display.inspector.InspectorPanelController
setExposure(double) - Method in interface org.micromanager.Application: Set the exposure time for the current channel (if any).
setFullScreen(boolean) - Method in interface org.micromanager.display.DisplayWindow: Enable or disable full screen mode.
setGeneralAnnotation(PropertyMap) - Method in interface org.micromanager.data.Annotation: Replace the data this Annotation has for the Datastore as a whole with the provided PropertyMap.
setGridCoordinates(int, int) - Method in class org.micromanager.MultiStagePosition: Sets grid parameters for the rectangular grid.
setImageAnnotation(Coords, PropertyMap) - Method in interface org.micromanager.data.Annotation: Replace the data this Annotation has for the specified Image with the provided PropertyMap.
setImageJName(String) - Method in interface org.micromanager.display.ImageExporter: Sets the name to be used for the ImageJ Stack Window (if this was used as the output format).
setInt(Class<?>, String, Integer) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putInteger(key, value) instead
setIntArray(Class<?>, String, Integer[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putIntegerList(key, value) instead
setLabel(String) - Method in class org.micromanager.MultiStagePosition: Sets position label (such as well name, etc.).
setLabel(int, String) - Method in class org.micromanager.PositionList: Assigns a label to the position index.
setLiveMode(boolean) - Method in interface org.micromanager.SnapLiveManager: Deprecated.
setLiveModeOn(boolean) - Method in interface org.micromanager.SnapLiveManager: Turns live mode on or off.
setLivePipelineStepEnabled(int, boolean) - Method in interface org.micromanager.data.DataManager: Sets whether or not the plugin at position `index` in the list is enabled for the live pipeline.
setLong(Class<?>, String, Long) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putLong(key, value) instead
setLongArray(Class<?>, String, Long[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putLongList(key, value) instead
setMagnification(double) - Method in interface org.micromanager.display.DisplayWindow: Deprecated.
use DisplayWindow.setZoom(double) instead
setName(String) - Method in interface org.micromanager.data.Datastore: Sets the name of the Datastore.
setOutputFormat(ImageExporter.OutputFormat) - Method in interface org.micromanager.display.ImageExporter: Set the output format to use.
setOutputQuality(int) - Method in interface org.micromanager.display.ImageExporter: Set the image quality.
setPause(boolean) - Method in interface org.micromanager.acquisition.AcquisitionManager: Pause/Unpause a running acquisition.
setPositionList(PositionList) - Method in interface org.micromanager.PositionListManager: Makes this the 'current' PositionList, i.e., the one used by the Acquisition Protocol, and shown in the PositionListDlg.
setPositions(MultiStagePosition[]) - Method in class org.micromanager.PositionList: Initialize the entire array by passing an array of multi-stage positions.
setProperty(PropertyItem) - Method in interface org.micromanager.AutofocusPlugin: Sets the value of a particular property.
setProperty(String, String) - Method in class org.micromanager.MultiStagePosition: Add a generalized property-value par to the position.
setPropertyValue(String, String) - Method in interface org.micromanager.AutofocusPlugin: Sets the value of a named property.
setROI(Rectangle) - Method in interface org.micromanager.Application: Set the default camera's ROI -- a convenience function.
setSaveInfo(String, String) - Method in interface org.micromanager.display.ImageExporter: Set the path to save images to, and the filename prefix to use when saving images.
setSavePath(String) - Method in interface org.micromanager.data.Datastore: Set the intended path where the data will be stored.
setShutter(boolean) - Method in interface org.micromanager.ShutterManager: Open or close the shutter.
setSkin(ApplicationSkin.SkinMode) - Method in interface org.micromanager.ApplicationSkin: Sets the background color of the GUI to the selected mode.
setStorage(Storage) - Method in interface org.micromanager.data.Datastore: Sets the data storage implementation for this Datastore.
setString(Class<?>, String, String) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putString(key, value) instead
setStringArray(Class<?>, String, String[]) - Method in interface org.micromanager.UserProfile: Deprecated.
use getSettings(c).putStringList(key, value) instead
setSummaryMetadata(SummaryMetadata) - Method in interface org.micromanager.data.Datastore: Set the SummaryMetadata.
setSummaryMetadata(SummaryMetadata) - Method in interface org.micromanager.data.RewritableDatastore: Set the SummaryMetadata.
setSuspended(boolean) - Method in interface org.micromanager.SnapLiveManager: Temporarily halt live mode, or re-start it after a temporary halt.
setText(String) - Method in interface org.micromanager.alerts.UpdatableAlert: Update the text displayed by the Alert.
setUseLabel(boolean) - Method in interface org.micromanager.display.ImageExporter: Whether to use labels indicating position, channel, time point and z position (where) appropriate or to sequentially number output files.
setVisible(boolean) - Method in class org.micromanager.display.overlay.AbstractOverlay: Show or hide this overlay.
setVisible(boolean) - Method in interface org.micromanager.display.overlay.Overlay: Show or hide this overlay.
setZoom(double) - Method in interface org.micromanager.display.DisplayWindow: Set the zoom ratio for this display.
shouldAutostretch(Boolean) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
shouldDisplayImages(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
shouldDisplayImages - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and shouldDisplayImages() instead
shouldDisplayImages() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to display acquired data.
shouldScaleWithROI(Boolean) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
shouldSyncChannels(Boolean) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
show() - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
show(Image) - Method in interface org.micromanager.display.DisplayManager: Create a new Datastore with an associated DisplayWindow that will display the provided Image.
show() - Method in interface org.micromanager.display.DisplayWindow: DisplayWindows are not shown by default.
showAutofocusDialog() - Method in interface org.micromanager.Application: Pop up the dialog used to configure the autofocus settings for the current autofocus device.
showBackgroundWindow(boolean) - Method in interface org.micromanager.Application: Shows a background window, that hides potentially cluttered desktops and provides a better look for the applictions
showError(Exception, String) - Method in interface org.micromanager.LogManager: Shows an error in the UI and logs stacktrace to the Micro-Manager log.
showError(Exception) - Method in interface org.micromanager.LogManager: Shows and logs a Java exception.
showError(String) - Method in interface org.micromanager.LogManager: Shows an error message in the UI and logs to the Micro-Manager log.
showError(Exception, String, Component) - Method in interface org.micromanager.LogManager: Shows an error in the UI and logs stacktrace to the Micro-Manager log.
showError(Exception, Component) - Method in interface org.micromanager.LogManager: Shows and logs a Java exception.
showError(String, Component) - Method in interface org.micromanager.LogManager: Shows an error message in the UI and logs to the Micro-Manager log.
showGUI() - Method in interface org.micromanager.data.ProcessorConfigurator: Display any GUI needed for performing configuration.
showMessage(String) - Method in interface org.micromanager.LogManager: Shows a message in the UI.
showMessage(String, Component) - Method in interface org.micromanager.LogManager: Shows a message in the UI.
showPanels() - Method in interface org.micromanager.quickaccess.QuickAccessManager: Show the Quick Access Panels.
showPositionList() - Method in interface org.micromanager.Application: Display the position list dialog.
ShutdownCommencingEvent - Interface in org.micromanager.events: This event posts when the user requests the program to shut down.
shutter() - Method in interface org.micromanager.Studio: Provides access to the ShutterManager for controlling the shutter state.
ShutterEvent - Interface in org.micromanager.events: This event posts when the shutter opens or closes.
ShutterManager - Interface in org.micromanager: This class provides access to the shutter controls, allowing you to open or close the shutter, as well as turn autoshutter on or off.
SimpleButtonPlugin - Class in org.micromanager.quickaccess: This plugin type is used for buttons that can be embedded in the Quick-Access Window.
SimpleButtonPlugin() - Constructor for class org.micromanager.quickaccess.SimpleButtonPlugin
size() - Method in class org.micromanager.MultiStagePosition: Number of stages.
size() - Method in interface org.micromanager.propertymap.MutablePropertyMapView: Return the number of keys in this view.
size() - Method in interface org.micromanager.PropertyMap
skin() - Method in interface org.micromanager.Application: Provides access to the application skin API for determining colors for various GUI components.
skipAutofocusCount(int) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
skipAutofocusCount - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and skipAutofocusCount() instead
skipAutofocusCount() - Method in class org.micromanager.acquisition.SequenceSettings: how many autofocus opportunities to skip.
skipFactorFrame(int) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
skipFactorFrame - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
skipFactorFrame() - Method in class org.micromanager.acquisition.ChannelSpec
slices(ArrayList<Double>) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
slices - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and slices() instead
slices() - Method in class org.micromanager.acquisition.SequenceSettings: Z- drive positions to be used to acquire a z-stack.
slicesFirst(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
slicesFirst - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and slicesFirst() instead
sliceZBottomUm(double) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
sliceZBottomUm() - Method in class org.micromanager.acquisition.SequenceSettings: Start position of the z-stack in microns.
sliceZStepUm(double) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
sliceZStepUm() - Method in class org.micromanager.acquisition.SequenceSettings: Distance the z-drive should travel between steps when acquiring a z-stack.
sliceZTopUm(double) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
sliceZTopUm() - Method in class org.micromanager.acquisition.SequenceSettings: End position of the z-stack in microns.
SLMExposureChangedEvent - Interface in org.micromanager.events: This interface posts when the exposure time for a given Spatial Light Modulator (such as a Digital Mirror Device) changes.
snap() - Method in interface org.micromanager.acquisition.AcquisitionManager: Snap images using the current camera(s) and return them.
snap(boolean) - Method in interface org.micromanager.SnapLiveManager: Perform a snap and display the results, if desired.
SnapLiveManager - Interface in org.micromanager: Interface for interacting with the Snap/Live display and live mode.
STAGE_POSITION - Static variable in interface org.micromanager.data.Coords: Axis label for the stage position axis.
stageName - Variable in class org.micromanager.StagePosition: Deprecated.
Use StagePosition.set1DPosition(java.lang.String, double) or StagePosition.set2DPosition(java.lang.String, double, double) to set; use StagePosition.getStageDeviceLabel() to access.
stagePosition(int) - Method in interface org.micromanager.data.Coords.Builder: Set the stage position index.
stagePosition(int) - Method in interface org.micromanager.data.Coords.CoordsBuilder
StagePosition - Class in org.micromanager: Description of the position of a 1 or 2 axis stage.
StagePosition() - Constructor for class org.micromanager.StagePosition: Deprecated.
Use StagePosition.create1D(java.lang.String, double) or StagePosition.create2D(java.lang.String, double, double) instead.
StagePositionChangedEvent - Interface in org.micromanager.events: This class signals when a single-axis drive has moved.
stagePositions(MultiStagePosition...) - Method in interface org.micromanager.data.SummaryMetadata.Builder
stagePositions(Iterable<MultiStagePosition>) - Method in interface org.micromanager.data.SummaryMetadata.Builder
stagePositions(MultiStagePosition...) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
startDate(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
startDate(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
StartupCompleteEvent - Interface in org.micromanager.events: This event signifies that the system finished starting up.
Storage - Interface in org.micromanager.data: Storages are responsible for providing image data to Datastores when requested.
Studio - Interface in org.micromanager: Interface to execute commands in the main panel.
SummaryMetadata - Interface in org.micromanager.data: This class defines the summary metadata that applies to all images in a dataset.
SummaryMetadata.Builder - Interface in org.micromanager.data: Builder for SummaryMetadata.
SummaryMetadata.SummaryMetadataBuilder - Interface in org.micromanager.data: Deprecated.
- Use SummaryMetadata.Builder instead
summaryMetadataBuilder() - Method in interface org.micromanager.data.DataManager: Generate a "blank" SummaryMetadataBuilder for use in constructing new SummaryMetadata instances.
suspendToMode(ApplicationSkin.SkinMode) - Method in interface org.micromanager.ApplicationSkin: If the specified mode is not currently active, then we switch to that mode without updating the UI.
SystemConfigurationLoadedEvent - Interface in org.micromanager.events: This interface signals when a configuration file is loaded.

T

t(int) - Method in interface org.micromanager.data.Coords.Builder: Shorthand for time.
T - Static variable in interface org.micromanager.data.Coords: Axis label for the time point (frame) axis (short form).
time(int) - Method in interface org.micromanager.data.Coords.Builder: Deprecated.
Due to being confusing with physical time.
time(int) - Method in interface org.micromanager.data.Coords.CoordsBuilder
TIME - Static variable in interface org.micromanager.data.Coords: Deprecated.
Use discouraged because it reads like a physical time rather than the time point index that it is.
TIME_POINT - Static variable in interface org.micromanager.data.Coords: Axis label for the time point (frame) axis.
timeFirst(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
timeFirst - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and timeFirst() instead
timePoint(int) - Method in interface org.micromanager.data.Coords.Builder: Set the time point (frame) index.
toFront() - Method in interface org.micromanager.display.DisplayWindow: Raise this display window to the front.
ToggleButtonPlugin - Class in org.micromanager.quickaccess: This plugin type is used for buttons that can be embedded in the Quick-Access Window.
ToggleButtonPlugin() - Constructor for class org.micromanager.quickaccess.ToggleButtonPlugin
toggleFullScreen() - Method in interface org.micromanager.display.DisplayWindow: Deprecated.
use DisplayWindow.setFullScreen(boolean) instead
toJSON() - Method in interface org.micromanager.PropertyMap: Create a JSON representation of this property map.
toJSONStream(ChannelSpec) - Static method in class org.micromanager.acquisition.ChannelSpec: Serialize to JSON encoded string.
toJSONStream(SequenceSettings) - Static method in class org.micromanager.acquisition.SequenceSettings
toPropertyMap() - Method in class org.micromanager.MultiStagePosition: Returns a propertymap describing this MultiStagePosition.
toPropertyMap() - Method in class org.micromanager.PositionList: Creates a PropertyMap from this PositionList.
toPropertyMap() - Method in interface org.micromanager.propertymap.MutablePropertyMapView: Return a property map copy of this view.
toPropertyMap() - Method in class org.micromanager.StagePosition: Returns this StagePosition instance as a PropertyMap.
toString() - Method in class org.micromanager.acquisition.ChannelSpec
toString() - Method in class org.micromanager.acquisition.SequenceSettings
toString() - Method in class org.micromanager.display.HistogramData: Deprecated.
toString() - Method in class org.micromanager.MultiStagePosition
toString() - Method in class org.micromanager.StagePosition
TypeMismatchException(String) - Constructor for exception org.micromanager.PropertyMap.TypeMismatchException: Deprecated.
Constructor should not have been part of API.

U

uniformChannelScaling(boolean) - Method in interface org.micromanager.display.DisplaySettings.Builder: Whether to use the same intensity scaling for every channel.
uniformComponentScaling(boolean) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
unregisterForEvents(Object) - Method in interface org.micromanager.data.DataProvider
unregisterForEvents(Object) - Method in class org.micromanager.display.AbstractDataViewer
unregisterForEvents(Object) - Method in interface org.micromanager.display.DataViewer
unregisterForEvents(Object) - Method in interface org.micromanager.EventPublisher: Unregister an object from the viewer event bus.
unregisterForEvents(Object) - Method in interface org.micromanager.events.EventManager: Un-register the provided object from the EventBus, so that it will no longer receive event notifications.
UpdatableAlert - Interface in org.micromanager.alerts: UpdatableAlerts are Alerts whose message texts can be changed after they have been posted.
useAutofocus(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
useAutofocus - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and useAutofocus() instead
useAutofocus() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to use autofocus before each time point / position.
useCameraHistoRange(boolean) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder
useCameraRange() - Method in interface org.micromanager.display.ChannelDisplaySettings: Returns whether the camera range is used as histogram range.
useChannel(boolean) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
useChannel - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
useChannel() - Method in class org.micromanager.acquisition.ChannelSpec
useChannels(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
useChannels() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to acquire multiple channels during the acquisition.
useCustomIntervals(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
useCustomIntervals - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and useCustomIntervals() instead
useCustomIntervals() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to use custom time intervals defined SequenceSettings.customIntervalsMs().
useFrames(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
useFrames() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to acquire multiple time points during the acquisition.
usePositionList(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
usePositionList - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and usePositionList() instead
usePositionList() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to acquire at multiple positions (defined in the positionList).
userData(PropertyMap) - Method in interface org.micromanager.data.Metadata.Builder: Add user-defined data.
userData(PropertyMap) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
userData(PropertyMap) - Method in interface org.micromanager.data.SummaryMetadata.Builder
userData(PropertyMap) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
userName(String) - Method in interface org.micromanager.data.SummaryMetadata.Builder
userName(String) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
UserProfile - Interface in org.micromanager: A user profile, where user preferences can be stored.
UserProfileMigration - Interface in org.micromanager.profile: Interface for object providing user profile setting migration.
UserProfileMigrator - Class in org.micromanager.profile: Automatically migrate user profile settings.
UserProfileMigrator() - Constructor for class org.micromanager.profile.UserProfileMigrator
useSlices(boolean) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
useSlices() - Method in class org.micromanager.acquisition.SequenceSettings: Whether to acquire z stacks during the acquisition.
uuid() - Method in interface org.micromanager.data.Metadata.Builder: Deprecated.
Use Metadata.Builder.generateUUID().
uuid(UUID) - Method in interface org.micromanager.data.Metadata.Builder
uuid() - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
uuid(UUID) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.

V

valueOf(String) - Static method in enum org.micromanager.ApplicationSkin.SkinMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.micromanager.data.Datastore.SaveMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.micromanager.display.DisplaySettings.ColorMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.micromanager.display.ImageExporter.OutputFormat: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.micromanager.ApplicationSkin.SkinMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.micromanager.data.Datastore.SaveMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.micromanager.display.DisplaySettings.ColorMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.micromanager.display.ImageExporter.OutputFormat: Returns an array containing the constants of this enum type, in the order they are declared.
Version - Static variable in class org.micromanager.acquisition.SequenceSettings
versionLessThan(String) - Method in interface org.micromanager.CompatibilityInterface: Displays an error message and returns true if the run-time Micro-Manager version is less than the one specified.
visible(boolean) - Method in interface org.micromanager.display.ChannelDisplaySettings.Builder

W

waitForExport() - Method in interface org.micromanager.display.ImageExporter: Block until a prior call to export() returns.
waitInterval(Double) - Method in interface org.micromanager.data.SummaryMetadata.Builder
waitInterval(Double) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.
WidgetPlugin - Class in org.micromanager.quickaccess: This plugin allows arbitrary controls ("widgets") to be included in the Quick-Access Window.
WidgetPlugin() - Constructor for class org.micromanager.quickaccess.WidgetPlugin
wrapImage(Object, int, int, int, int, Coords, Metadata) - Method in interface org.micromanager.data.DataManager: Generate a new Image with the provided pixel data, rules for interpreting that pixel data, coordinates, and metadata.

X

x - Variable in class org.micromanager.StagePosition: Deprecated.
Use methods instead.
xPositionUm(Double) - Method in interface org.micromanager.data.Metadata.Builder
xPositionUm(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
XYStagePositionChangedEvent - Interface in org.micromanager.events: This class signals when any XY stage changes position.

Y

y - Variable in class org.micromanager.StagePosition: Deprecated.
Use methods instead.
yPositionUm(Double) - Method in interface org.micromanager.data.Metadata.Builder
yPositionUm(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.

Z

z(int) - Method in interface org.micromanager.data.Coords.Builder: Shorthand for Coords.Builder.zSlice(int).
z(int) - Method in interface org.micromanager.data.Coords.CoordsBuilder
Z - Static variable in interface org.micromanager.data.Coords: Axis label for the Z slice axis (short form).
z - Variable in class org.micromanager.StagePosition: Deprecated.
Z_SLICE - Static variable in interface org.micromanager.data.Coords: Axis label for the Z slice axis.
zOffset(double) - Method in class org.micromanager.acquisition.ChannelSpec.Builder
zOffset - Variable in class org.micromanager.acquisition.ChannelSpec: Deprecated.
Use Builder and getters instead
zOffset() - Method in class org.micromanager.acquisition.ChannelSpec
zoom(Double) - Method in interface org.micromanager.display.DisplaySettings.DisplaySettingsBuilder: Deprecated.
zoomRatio(double) - Method in interface org.micromanager.display.DisplaySettings.Builder
zPositionUm(Double) - Method in interface org.micromanager.data.Metadata.Builder
zPositionUm(Double) - Method in interface org.micromanager.data.Metadata.MetadataBuilder: Deprecated.
zReference(double) - Method in class org.micromanager.acquisition.SequenceSettings.Builder
zReference - Variable in class org.micromanager.acquisition.SequenceSettings: Deprecated.
use Builder and zReference() instead
zReference() - Method in class org.micromanager.acquisition.SequenceSettings: referent z position for relative moves.
zSlice(int) - Method in interface org.micromanager.data.Coords.Builder: Set the Z slice index.
zStepUm(Double) - Method in interface org.micromanager.data.SummaryMetadata.Builder
zStepUm(Double) - Method in interface org.micromanager.data.SummaryMetadata.SummaryMetadataBuilder: Deprecated.

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