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Revision as of 14:12, 18 August 2014 by Mark Tsuchida (Talk | contribs)

(Previous releases)

Micro-Manager 1.4.18 (July 31, 2014)

Windows 32-bit, 57 MB
Windows 64-bit, 59 MB

Mac OS X (Universal Binary), 44 MB
(OS X 10.8 or later: if the application does not open when double-clicked for the first time, try ctrl-click or right click, then select "Open".)

Known issues in 1.4.18

  • PCO_Camera: There is an issue with setting the ROI with some cameras (pixelfly QE, pixelfly vga, pco.pixelfly_USB, pco.1300, pco.1300 solar, pco.1400, pco.ultraviolet). If you are affected, replace the mmgr_dal_PCO_Camera.dll file in the Micro-Manager folder with the version available here (for 32-bit MM) or here (for 64-bit MM). The issue is also fixed in nightly builds since 20140801.
  • Hang when Position List window is open: This can happen (usually during an MDA) with certain devices (e.g. NikonTI). Closing the Position List before starting an acquisition should prevent the hang. Fixed in nightly build of 20140818.

Changes in 1.4.18 (since 1.4.17)

  • New in the main application
    • Improvements to the image display window:
      • Added ability to animate any dataset axis, not just time/Z (Chris Weisiger)
      • Added "superlock" mode to image display windows (click on the lock icon twice) to prevent new images from changing the display at all (Chris Weisiger)
      • Added display of intensity of pixel under the mouse (Chris Weisiger, Jon Daniels)
      • Various layout tweaks
    • Improvements to the Stage Position List dialog (Chris Weisiger):
      • Automatically update the stage position when it moves.
      • Improved behavior of "Merge" button
      • Added "Add Offset" button to add a fixed offset to selected positions.
    • Improvements to the Options dialog (Mark Tsuchida):
      • Improved layout
      • Removed nonfunctional "autoreload devices" checkbox from Options dialog
      • Save options when dialog is closed via close box
      • Add confirmation before resetting preferences
      • Add ability to automatically delete old log files
    • Added "Image Pipeline" dialog (via the Tools menu) for configuring the image data processing pipeline (Chris Weisiger)
    • Correctly show "Galvo" devices in Device Wizard (Jon Daniels)
    • Improved the Problem Report to provide more information (Mark Tsuchida)
    • Added a warning, prior to running pixel calibration, that the stage will move (Mark Tsuchida)
    • Ensure windows and dialogs don't load off-screen (Jon Daniels, Chris Weisiger)
    • Multipage TIFF files don't write multiple copies of the OME metadata, improving performance/filesizes (Henry Pinkard)
    • Multipage TIFF files include an index map at the beginning of the file (Henry Pinkard)
    • Include pixel type in acquisition metadata (Mark Tsuchida)
    • CoreLog files are now saved in a CoreLogs folder, and a new file is created each time Micro-Manager is started (Mark Tsuchida)
    • Generating a Problem Report no longer has the side effect of clearing the usual CoreLog file (Mark Tsuchida)
    • In hardware-triggered MDA, avoid reloading sequences to devices when not necessary (Arthur Edelstein)
    • Bug fixes:
      • Fixed bug in data saving that caused metadata.txt to be incomplete (Mark Tsuchida)
      • Fixed memory leak when running acquisitions or opening/closing files (Chris Weisiger)
      • Fixed a bug that could cause the display to freeze (Chris Weisiger, Mark Tsuchida)
      • Fixed bug causing spurious error messages when closing the display (Chris Weisiger, Nico Stuurman)
      • Fixed a null pointer exception when drawing multi-camera images (Nico Stuurman)
      • Fixed various bugs when closing acquisitions (Henry Pinkard, Mark Tsuchida)
      • Fixed bug #686 (Autoscale settings are applied inconsistently) (Chris Weisiger)
      • Fixed a bug causing the "Hide MDA Display" option to not be remembered across sessions (Chris Weisiger)
      • Fixed a bug when setting camera ROIs (Mark Tsuchida)
      • Fixed an occasional bug during startup when initializing Beanshell (Mark Tsuchida)
      • Opening ImageJ64.app on OS X 10.8 or later no longer results in an "application damaged" error (Mark Tsuchida)
  • New plugins
    • Sequence Buffer Monitor: displays memory utilization in the sequence buffer, which can help in optimizing the buffer size (Mark Tsuchida)
  • Updated plugins
    • Acquire Multiple Regions: Allow radially weighted interpolation between different Z coordinates in a region (Kurt Thorn)
    • ASI diSPIM: Numerous engancements and fixes (Jon Daniels, ASI; Nico Stuurman)
    • ASI CRISP: Support TG-1000 "Tiger" CRISP (Jon Daniels, ASI)
    • Pixel Calibrator: Return to original position and re-acquire image after calibration (Falk Dettmar)
    • Projector: Enhancements and fixes for SLM ROI support (Arthur Edelstein for Andor)
  • New device adapters
    • CoherentOBIS: Coherent OBIS laser controllers (Forrest Collman)
    • NewportSMC: Newport SMC100 motor controller (Liisa Hirvonen, submitted by Newport)
    • PicardStage: Picard Industries USB 4D stage (Johannes Schindelin and Luke Stuyvenberg)
  • Updated device adapters
    • Andor: Update to use latest Andor driver, add iXon 888 isolated crop ROIs (Matthew Milford, Andor)
    • AndorSDK3: Fix a crash or hang that could occur when rapidly stopping and restarting a sequence acquisition (Norman Glasgow, Andor)
    • Arduino: Fix an issue when using multiple Arduinos (Nico Stuurman)
    • ASIStage: Add acceleration and firmware version properties, add support for turrets and sliders, correctly detect stage when using 115200 baud, improve wait cycles handling (Jon Daniels, ASI); fix CRISP gain setting (Nico Stuurman)
    • ASITiger: Add support for LED illuminators, add stage wheel speed (firmware 2.87+) property, allow XY stage to be split across two cards, support for firmware 2.88 features, various fixes (Jon Daniels, ASI)
    • BaumerOptronic: Prevent high CPU usage, fix issue with sequence acquisition following ROI change (Eugene Dvoretsky); prevent stale images from being returned and avoid constantly running camera (Mark Tsuchida)
    • dc1394: On windows, update to libdc1394 2.2.1 and support 64-bit (Mark Tsuchida)
    • DemoCamera: Add "rotate image" mode (Chris Weisiger); remove some hard-to-correctly-use testing-related features (Mark Tsuchida)
    • IIDC: Do not reject 1394A cameras, do not skip by default in Linux build (Mark Tsuchida)
    • Ludl: Allow setting of XY step sizes independently (Nico Stuurman)
    • MCL_MicroDrive: Add support for MicroDrive3 and MicroDrive1 (Greg Sawyer, MCL)
    • NewportCONEX: Renamed from CONEX.
    • Okolab: Fix issue with port selection, add active humidifier device support (Marco Di Pasqua, Okolab)
    • PCO_Camera: Fix ROI ROI handling issues, add support for external triggering, various fixes (Franz Reitner, PCO)
    • pgFocus: Add Windows support, bugfixes (Karl Bellvé)
    • Piezosystem_NV40_1, Piezosystem_NV40_3, Piezosystem_NV120_1: Prevent error during MDA (Mark Tsuchida)
    • PVCAM: Limit range of ClearCycles property, fix handling of property settings, bugfixes (Lubomir Walder, Photometrics)
    • SerialManager: Prevent a crash or error when connecting to certain USB-serial interfaces that use Silicon Labs chips (e.g. ASI controllers) on certain Windows systems (Mark Tsuchida)
    • Tofra: Fix state device State and Label properties and channel intensity properties (Mark Tsuchida); fix issue with filter wheel positioning (Ilya Ravkin, Tofra)
    • VariLC: Fix a "property name contains reserved chars" error, add properties for absolute retardance and variable time delay (Amitabh Verma)
    • VersaLase: Add support for VersaLase devices with up to 4 lasers (David Sweeney, Vortran)
  • New closed-source device adapters
  • Updated closed-source device adapters
    • AxioCam: Prevent spurious ROI change after changing binning (Mark Tsuchida)
    • HamamatsuHam: Added new properties for trigger and line speed control (Patrick Gregorio, Hamamatsu); fixed an issue that caused hardware-triggered MDA to fail (Nico Stuurman)
    • Hamamatsu (OS X): Removed 64-bit version, which was not functional (Mark Tsuchida)
    • Mosaic3: Bugfixes (Arthur Edelstein for Andor)
  • Changes to the scripting/Java API
    • Added new Plugin type, MMProcessorPlugin, for plugins whose purpose is to examine/modify image data in the Image Processor pipeline. See https://micro-manager.org/wiki/Writing_image_processors_for_Micro-Manager for more details. (Chris Weisiger)
    • Added the Guava library's Event Bus. Objects can be registered for callbacks using gui.registerForEvents(); see the org.micromanager.api.events package for the list of events that are available. Remember to annotate your functions with @Subscribe.
    • Added API functions getImageProcessorPipeline() and setImageProcessorPipeline() (Chris Weisiger)
    • Added API function setAcquisitionAddImageAsynchronous(acquisitionName). This will speed up future calls to gui.addImageToAcquisition(). (Chris Weisiger)
    • Added API function getCacheForWindow(ImageWindow) which will return the associated ImageCache. (Chris Weisiger)
    • Added new core callback function OnSLMExposure() for when an SLM's exposure time changes (Arthur Edelstein)
    • When opening a file from the GUI, the "acquisition" used to load the file data is left resident in memory, allowing its data to be accessed e.g. via gui.getAcquisitionImageCache() (Nico Stuurman)
  • Changes to the MMCore API
    • MMCore version number is once again maintained (Micro-Manager 1.4.18 ships with MMCore 5.0.3)
    • MMEventCallback now has an onSLMExposureChanged() member function (Arthur Edelstein)
    • New logging management API (setPrimaryLogFile(), getPrimaryLogFile(), startSecondaryLogFile(), stopSecondaryLogFile(), stderrLogEnabled()) (Mark Tsuchida)
    • New getCircularBufferMemoryFootprint() function (Mark Tsuchida)
    • The following functions are deprecated and will be removed in the next release: clearLog(), saveLogArchive(), saveLogArchiveWithPreamble(), getBufferIntervalMs()
  • Changes to the MMDevice API
    • Micro-Manager 1.4.18 requires module interface version 10, device interface version 60.
    • The previously deprecated AddavailableDeviceName() function has been removed (use RegisterDevice())
    • Class hierarchy changed for "generic" devices (should not affect device adapter code unless CDeviceBase internals are accessed)
    • CDeviceBase::GetPortType() was renamed to GetSerialPortType() to avoid name clash
    • g_Keyword_Metadata_Z has been removed (probably never used)
    • SLM devices now can issue a notification when the exposure changes
    • MMDevice no longer depends on Boost headers
    • Device types that were never supported have been removed (CommandDispatch, ProgrammableIO, ImageStreamer)
  • Changes of interest to developers
    • Micro-Manager 1.4.18 is SVN trunk r13943, 3rdpartypublic r169.
    • Removed default access to private members in Beanshell scripts. Call setAccessibility(true) if you need to restore access. (Mark Tsuchida)
    • Allow plugins in .class files to be loaded, as long as they are not in packages. (Mark Tsuchida)
    • Removed many functions from MMStudioMainFrame that were never used nor exposed in the API. If you have code that relied on one of these methods, let us know. (Chris Weisiger)
    • VirtualAcquisitionDisplay has been extensively refactored and moved to the org.micromanager.imagedisplay package. However, if you rely on this module, please let us know, because ideally you shouldn't need to. (Chris Weisiger)
    • As part of a project to make the Core object-oriented, MMCore has been refactored to use DeviceInstance objects to manage access to devices (Mark Tsuchida)
    • The Core logger (which produces CoreLog) has been completely rewritten, and should longer drop entries during shutdown (Mark Tsuchida)
    • Core logging to stderr and the primary log file is not enabled upon CMMCore instantiation; it is explicitly enabled by the application (Mark Tsuchida)
    • Building using Ant on Windows now requires running ant -f buildscripts/fetchdeps.xml beforehand to download Ant extensions


(Previous releases)

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