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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.
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.
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.
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.
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.
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
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.
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.
getIsLiveModeOn() - Method in interface org.micromanager.SnapLiveManager
Deprecated.
getIsMainExposureTime() - Method in interface org.micromanager.events.ChannelExposureEvent
getIsManaged(DataProvider) - Method in interface org.micromanager.display.DisplayManager
getIsOn() - Method in interface org.micromanager.events.LiveModeEvent
Deprecated.
getIsSynchronous() - Method in interface org.micromanager.data.Pipeline
Deprecated.
getIsVisible() - Method in interface org.micromanager.display.DisplaySettings.ContrastSettings
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.
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
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.
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
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.
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.
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.
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
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
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
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
putInt(String, Integer) - Method in interface org.micromanager.PropertyMap.PropertyMapBuilder
Deprecated.
putIntArray(String, Integer[]) - Method in interface org.micromanager.PropertyMap.Builder
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
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
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
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.
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.
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.
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.
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.
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
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
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.
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.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
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
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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