Short Description

Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy !
Compatible with Micro-Manager 1.4.19 or above but we recommend to use the last Micro-Manager 1.4 (1.4.23 / nightly builds)

Team: Bio Image Analysis Unit
Institution: Institut Pasteur
Website: https://icy.bioimageanalysis.org
Source code: https://gitlab.pasteur.fr/bia/micro-manager-for-icy

Documentation

Be able to use your microscope and microscopic devices in Icy ! Thanks to the Micro-Manager for Icy plugin, you will be able to run all Microscope Plugins developed for Icy. That way, you will be able to capture images, watch a live video of your samples, and fully control your microscope. Why is it better to do it in Icy ? Because with its powerful Sequences and Lookup Table, Icy provides unique easy-to-use tools to work with your microscope. This is mostly used for fluorescence microscopy, as this plugin only works on one channel.

This plugin is based on Micro-Manager© v1.4.23 (current last version) but should be compatible with older versions back to  1.4.19
It runs every microscope and microscopic device supported by Micro-Manager. The list of all devices is available here.

Micro-Manager for Icy is a unique plugin because its installation is more sophisticated than for the other plugins. For instance, this is a Live 3D  video :

Please follow the Installation section below for more information.

Installation

  1. To install this plugin, just type “microm” in the search bar, you should see the Micro Manager plugin in the result list. Click on it to install it.
  2. On first launch, the plugin will ask for the folder the Micro Manager software. If you don’t have it you can install it from here else verify you have at least Micro-Manager v1.4.19. When it’s done, just give the installation folder information :
    1. Windows: C:\Program Files\Micro-Manager-1.4 or C:\Program Files (x86)\Micro-Manager-1.4 according to the version you are currently using (32 or 64-bit version).
    2. Mac: Applications/Micro-Manager
  3. As soon the plugin find Micro Manager, it will load all the libraries (it can takes some seconds) and be ready to use the Micro Manager features !

GUI Description

  • GUI is very close to classic Micro-Manager application except we removed useless parts as Histogram and Metadata which are already present in the default Icy GUI.
  • Don’t get lost, the configuration is based on Micro-Manager: simply change the preset by clicking on it.
  • Add / Remove / Edit configuration groups.
  • Add / Remove / Edit configuration presets.
Camera Settings
  1. Choose your own exposure.
  2. Change your own binning (from 1 to 4).
  3. Select the shutter you want to use
  4. Display the histogram according to the bit depth you are currently using. That way you will be able to set your exposure for your camera in order to take the best pictures.
Informations
Display setting informations about current acquisition.
Actions
Default Micro-Manager action to enable Live / Snap / Album or Advanced Acquisition
Extra Snap / Live / Album setting
Used to do 3D (Z Stack) Live or Snap / Album acquisition. Using the 3D volume rendering from VTK you can then directly obtain a 3D live display =)
You can find more information about Micro-Manager plugin in this tutorial:
https://icy.bioimageanalysis.org/doc/icy-micro-manager.pdf

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3 reviews on “Micro-Manager for Icy”

  2. S
    Sebastian Karpf
    Dear Thomas and Stephane, first I want to say a big thank you for the great work. I enjoy ICY a lot, it's such a wonderful tool. I was wondering wether Micro-Manager 2.0 will be supported in the future? Is there any plan on this? Thank you, Nino
    1. Stephane Dallongeville
      Thanks for your very kind message about Icy ! A Micro-Manager 2 plugin is not planned for now but as the question happen more and more we are starting to think about it ;)
      RATED

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Changelog

  • Version 1.9.6.0 • Released on: 2022-09-14 09:00:00
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    Description:

    Fixed configuration group / preset refresh

  • Version 1.9.5.0 • Released on: 2022-01-24 16:00:00
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    Description:

    - added new addCoreListener() / removeCoreListener() to get core event (registerCoreEvent(..) cannot be directly used)
    - properly forward core event to parent MMEventCallback (need to check that don't break anything)

  • Version 1.9.4.0 • Released on: 2021-11-17 17:15:00
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    Description:

    - fixed patching to make it compatible with Java 17
    - fixed dependencies so we don't require the duplicated from Micro-Manager

  • Version 1.9.3.0 • Released on: 2021-09-27 11:00:00
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    Description:

    Fixed config refresh + minors changes

  • Version 1.9.1.0 • Released on: 2021-03-16 16:00:00
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    Description:

    Updated About dialog (added citation references)

  • Version 1.9.0.0 • Released on: 2020-11-12 17:00:00
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    Description:

    Added acquisition name configuration

  • Version 1.8.0.0 • Released on: 2019-01-22 18:06:32
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    Description:

    Added color camera support (experimental)

  • Version 1.7.6.0 • Released on: 2018-12-10 14:39:11
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    Description:

    Added position information in Sequence name when doing multi position Multi Dimension acquisition.

  • Version 1.7.5.0 • Released on: 2018-07-16 10:43:46
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    Description:

    Safer access to Micro-Manager properties / methods

  • Version 1.7.4.0 • Released on: 2018-06-21 10:27:49
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    Description:

    Fixed binning set property in Micro-Manager.

  • Version 1.7.3.0 • Released on: 2018-06-08 16:46:47
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    Description:

    Fixed a small bug with Camera binning property

  • Version 1.7.2.1 • Released on: 2018-05-24 14:45:50
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    Description:

    Viewer from Multi-D acquisition now always go to last acquired image.

  • Version 1.7.2.0 • Released on: 2017-07-11 11:18:21
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    Description:

    * fixed possible crash when no camera defined

  • Version 1.7.1.5 • Released on: 2017-04-13 18:00:03
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    Description:

    reintroduced missing resource

  • Version 1.7.1.4 • Released on: 2017-04-13 17:55:50
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    Description:

    Rebuilded to fix the "method not found exception".

  • Version 1.7.1.3 • Released on: 2017-04-13 17:55:13
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    Description:

    Regression from version 1.7.1.1

  • Version 1.7.1.2 • Released on: 2017-04-13 17:54:35
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    Description:

    Rebuilded to fix the "method not found exception".

  • Version 1.7.1.1 • Released on: 2017-04-13 17:52:43
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    Description:

    Rebuilded to fix some method not found exception.

  • Version 1.7.1.0 • Released on: 2016-07-20 19:04:14
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    Description:

    * Major rewrote of the GUI to mimic the original uManager.
    * Better retrieval of metadata.
    * Live, Live 3D, Album and Advanced Acquisition are now directly included.
    * Added to control more options from original uManager.
    * Many bug fixes and other improvements.

  • Version 1.7.0.0 • Released on: 2016-07-20 18:38:52
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    Description:

    * Major rewrote of the GUI to mimic the original uManager.
    * Added to control more options from original uManager.
    * Live, Live 3D, Album and Advanced Acquisition are now directly included.
    * Many bug fixes and other improvements.

  • Version 1.6.1.1 • Released on: 2016-02-19 18:38:20
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    Description:

    fixed required java version.

  • Version 1.6.1.0 • Released on: 2016-02-19 18:28:33
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    Description:

    Fixed some dead lock issues.

  • Version 1.6.0.4 • Released on: 2016-02-12 18:29:38
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    Description:

    better error handling

  • Version 1.6.0.3 • Released on: 2016-02-12 18:24:36
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    Description:

    minor bug fix.

  • Version 1.6.0.2 • Released on: 2016-02-12 18:19:56
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    Description:

    fix minor issue

  • Version 1.6.0.1 • Released on: 2016-02-12 18:16:07
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    Description:

    fixed minor issue.

  • Version 1.6.0.0 • Released on: 2016-02-12 18:04:19
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    Description:

    * updated to support last Micro-Manager version
    * added camera / image information
    * several bug fixes

  • Version 1.5.6.1 • Released on: 2016-02-05 15:33:31
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    Description:

    Fixed error on missing methods for MM 1.4.16 and MM 1.4.17

  • Version 1.5.6.0 • Released on: 2016-01-28 17:24:38
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    Description:

    - some fixes on bpp image creation
    - better MM version error handling

  • Version 1.5.5.0 • Released on: 2015-10-22 18:49:37
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    Description:

    Better handling of incorrect MM version.

  • Version 1.5.4.0 • Released on: 2015-10-13 18:11:17
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    Description:

    - updated to last Bio-Formats (new unit API)
    - fixed some bugs

  • Version 1.5.3.1 • Released on: 2014-08-25 16:58:00
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    Description:

    Fixed error message on cancel operation.

  • Version 1.5.3.0 • Released on: 2014-08-22 18:03:00
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    Description:

    - Support for multi channel camera acquisition.
    - Many other changes, improvements and fixes.

  • Version 1.5.2.0 • Released on: 2014-07-15 11:33:17
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    Description:

    Minors fixes, tweak and refactoring.

  • Version 1.5.1.0 • Released on: 2014-07-10 14:04:44
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    Description:

    * Reverted to MicroManager main class name.
    * some tweaks and fixes.

  • Version 1.5.0.1 • Released on: 2014-07-03 22:47:23
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    Description:

    Fixed AWT thread issue.

  • Version 1.5.0.0 • Released on: 2014-07-03 22:17:41
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    Description:

    Complete rewrite of the plugin.
    Now auto detect the Micro Manger folder and use dynamic lbrary loading (don't require anymore the micro manager lib plugin).
    Many general improvements, should have better compatibility and work faster.

    Compatible with Micro Manager 1.4.15 or above.

  • Version 1.4.1.2 • Released on: 2014-06-12 16:38:13
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    Description:

    - Micro Manager folder detection.
    - Fixed minor issue on binning combo box.

  • Version 1.4.1.1b • Released on: 2013-09-24 17:43:36
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    Description:

    Updated to the last version of Micro-Manager : 1.4.15

  • Version 1.4.1.0 • Released on: 2013-08-26 10:11:01
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  • Version 1.4.0.0 • Released on: 2013-06-05 18:06:24
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    Description:

    * Now Handles better the metadata :
    - pixel size X / Y / Z
    - exposure
    - channel names

    Coming Soon :
    - time of acquisition
    - Time interval

  • Version 1.3.0.0 • Released on: 2013-04-09 17:47:23
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    Description:

    * Now fully functionnal with 1.4.14!

  • Version 1.2.2.2 • Released on: 2013-03-18 10:27:18
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  • Version 1.2.2.1 • Released on: 2013-02-25 17:48:52
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    Description:

    * updated for script editor last version

  • Version 1.2.2.0 • Released on: 2013-02-19 11:03:50
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    Description:

    * better support of Scripting.

  • Version 1.2.1.1 • Released on: 2013-01-25 17:42:04
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    Description:

    * corrected issue on loading previous file
    * needs testing ! notifyConfigAbout/Changed should work better

  • Version 1.2.1.0 • Released on: 2013-01-25 16:38:23
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    Description:

    * Sends more signals to plugins if they need them.

  • Version 1.2.0.0 • Released on: 2013-01-22 16:28:44
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    Description:

    * now automatically loads last file

  • Version 1.1.0.0 • Released on: 2013-01-16 11:47:13
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    Description:

    * now automatically last opened file
    * corrected "loading frame" issue with size
    * corrected dipose() / delete() issue that appeared in 1.3

  • Version 1.0.3.8 • Released on: 2013-01-15 16:54:13
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    Description:

    * Now prevents creating a sequence with a pixel size = 0.

  • Version 1.0.3.7 • Released on: 2013-01-11 15:51:21
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    Description:

    * updated for last kernel
    * small change in closing.

  • Version 1.0.3.6 • Released on: 2013-01-07 11:14:59
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    Description:

    Corrected an issue with the closing, should not have a memory leak now.

  • Version 1.0.3.5 • Released on: 2012-12-10 17:01:38
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    Description:

    Too early function call corrected, since new release is not available.

  • Version 1.0.3.4 • Released on: 2012-12-05 17:15:59
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    Description:

    Until a stable version working with 1.4.13 is released, few corrections with 1.4.10:
    - drag fixed
    - painters back for now
    - absolute histogram fixed

  • Version 1.0.3.3 • Released on: 2012-06-26 15:44:36
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    Description:

    removed a useless interface

  • Version 1.0.3.2 • Released on: 2012-05-24 14:50:26
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    Description:

    * StageMover corrected: will not prevent application from closing.

  • Version 1.0.3.1 • Released on: 2012-05-22 17:58:10
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    Description:

    Small modifications for a better compatibility with other microscopy plugins.

  • Version 1.0.3.0 • Released on: 2012-05-15 17:18:43
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    Description:

    * Updated to last version of µManager 1.4.10.

    * Painters are not visible anymore, they will be reimplemented soon as Daemon Plugins.

    * Please do not forget to update needed files along with the update of the plugin (thus, install the last version of µManager to get them).

  • Version 1.0.2.3 • Released on: 2012-04-16 14:05:49
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    Description:

    * inversion of Z
    * switch X and Y (if camera rotated 90°)

  • Version 1.0.2.2 • Released on: 2012-03-05 14:23:22
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    Description:

    Small fix concerning exitlistener error.

  • Version 1.0.2.0 • Released on: 2012-01-16 11:30:06
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    Description:

    Updated to 1.2

  • Version 1.0.1.2 • Released on: 2011-11-16 13:17:31
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  • Version 1.0.1.0 • Released on: 2011-11-09 15:26:26
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    Description:

    Updated to be fully compatible with last Icy version.

    Painters added: now you have painters on all sequences, containing information about the position.

  • Version 1.0.0.2 • Released on: 2011-09-22 16:42:19
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  • Version 1.0.0.1 • Released on: 2011-09-22 14:44:06
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    Description:

    Small fix: no more refresh issue when closing the window while no plugin is active.

  • Version 1.0.0.0 • Released on: 2011-09-22 14:32:07
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