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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 !
Compatible with Micro-Manager 1.4.19 or above but we recommend to use the current last (1.4.22)

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 based on Micro-Manager© v1.4.22 (current last version) but should be compatible with olders versions back to  1.4.19.
It runs every microscope and microscopic device supported by Micro-Manager. 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, 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 =)