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Fabrice de Chaumont
27 Feb 2013 16:39
Great great great, and great.

Micro-Manager for Icy

by Thomas Provoost

Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy! Now compatible with MM 1.4.14.
Publication Id
ICY-D7G9B7
See technical details
View complete changelog

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 now based on Micro-Manager© v1.4.14. It runs every microscope and microscopic device supported by Micro-Manager under this version. The list of all devices is disponible 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, please go the the tab "plugin" in the Icy ribbon and select "Online Plugins"
  2. Click on Micro-Manager for Icy in the list, and then click on "Install"
  3. Good, now you have the plugin installed in Icy, but before you start using it, you need Micro-Manager's files
  4. If you already have Micro-Manager installed in v1.4.10, please go to the step 5
    1. Micro-Manager is usually installed in:
      1. Windows: C:Program FilesMicro-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: ApplicationsMicro-Manager
    2. To know your current Micro-Manager version, please load Micro-Manager. On the introduction screen (where you choose your file), you will see: MMStudio v1.x.x
    3. If your version is not 1.4.10, please download it here.
  5. Please go to the installation directory (see 4.a) and copy:
    1. Windows: all the .dll files
    2. Mac: libMMCoreJ_wrap.jnilib and all files starting by "libmmgr_dal_"
  6. Now paste those files into the Icy directory.

GUI Description

Configuration

  1. Use tabs to easily switch from different panels.
  2. Don't get lost, the configuration is based on Micro-Manager: simply change the preset by clicking on it.
  3. Add / Remove / Edit configuration groups.
  4. Add / Remove / Edit configuration presets.
Camera Settings
  1. Use tabs to easily switch from different panels.
  2. Choose your own exposure.
  3. Change your own binning (from 1 to 4).
  4. Select the shutter you want to use
  5. 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.
Running Acquisitions
  1. Use tabs to easily switch from different panels.
  2. An acquisition is currently running. Its progress is shown with a percentage.
  3. Whenever Micro-Manager uses a continuous acquisition instead of snaps, this bar is shown. For instance, this bar is visible when you run the Microscope Live plugin.