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Revision as of 13:38, 6 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.

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 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 for more details. (Chris Weisiger)
    • Added the Guava library's Event Bus. Objects can be registered for callbacks using gui.registerForEvents(); see the 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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