Short Description

Use Icy as an image viewer from Matlab. This plugin provides an improved imshow function, called icy_imshow, to replace the default Matlab viewer by Icy. It also provides some tools to display video sequences and 3D images in Icy.

Documentation

Quick start

This plugin allows you to use Icy as an image and/or video viewer for Matlab. It works as follows:

  1. First, install the plugin in Icy. This operation will create several Matlab function files (all named icy_someaction.m) in the plugin folder, which is located at /path/to/Icy/plugins/ylemontag/matlabxserver.
  2. Reference this folder in your Matlab path environment variable, so that the icy_someaction functions become callable from the Matlab command window. To do that, you must follow the install procedure for the Matlab communicator plugin, described at https://icy.bioimageanalysis.org/plugin/Matlab_communicator.
  3. Use the icy_someaction functions to display images and/or video. For example, to display a 2D image, execute the following command (you must have a running instance of Icy for this to work):
    >> im = phantom(512);
    >> icy_imshow(im, 'Shepp-Logan phantom');

Enjoy!

Available functions

Please notice that a detailed documentation is provided for each of these Matlab functions in the corresponding .m files. You can consult it directly from the Matlab help browser.

  • icy_imshow : display a 2D image
  • icy_im3show : display a 3D image
  • icy_vidshow : display a 2D video sequence
  • icy_vid3show : display a 3D video sequence
  • icy_close : close a viewer previously opened using one of the previous functions
  • icy_closeall : close all the viewers previously opened from Matlab
  • icy_gettitle and icy_settitle : retrieve or change the title of a viewer
  • icy_rectangle : create and display a rectangle ROI onto a previously opened sequence
  • icy_line : create and display a line ROI onto a previously opened sequence
  • icy_clearroi : hide a ROI
  • icy_synclut : synchronize the lookup-tables (i.e. the colormap, in the Matlab terminology) used to display images and video sequences
  • icy_syncnav : synchronize the navigation between several viewers displaying images and video sequences
  • icy_roimask : ask the user to create a ROI on a previously displayed image or video sequence, and return the corresponding boolean mask (this is the equivalent of the Matlab built-in roipoly function)

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Changelog

  • Version 3.2.0.0 • Released on: 2013-05-17 18:17:47
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    Description:

    Fix: icy_mask renamed in icy_roimask (there will be icy_roirectangle, icy_roiline, etc... methods in the future, to force the user to select a certain type of ROI). Also, use the class Overlay instead of Painter.

  • Version 3.1.0.0 • Released on: 2013-02-12 16:06:00
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    Description:

    Add: icy_mask() function, to replace the Matlab built-in function roipoly().

  • Version 3.0.0.0 • Released on: 2012-10-12 11:48:01
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    Description:

    Add: new communication protocol between Matlab and Icy, using the Matlab communicator plugin.

  • Version 2.5.1.0 • Released on: 2012-07-10 16:11:45
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    Description:

    Fix: Extraction procedure for .m files

  • Version 2.5.0.0 • Released on: 2012-07-10 15:39:16
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    Description:

    Add: new functions icy_rectangle and icy_line to create ROIs from Matlab.

  • Version 2.4.7.0 • Released on: 2012-07-03 09:49:29
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    Description:

    Fix: implement the new PluginDeamon interface.

  • Version 2.4.6.0 • Released on: 2012-06-27 16:29:55
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    Description:

    Fix: Same issue than version 2.4.3.

  • Version 2.4.5.0 • Released on: 2012-06-27 16:05:32
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    Description:

    Fix: Same issue than version 2.4.3

  • Version 2.4.4.0 • Released on: 2012-06-27 15:59:32
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    Description:

    Fix: ThreadUtil.sleep() instead of wait()

  • Version 2.4.3.0 • Released on: 2012-06-27 15:54:29
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    Description:

    Fix: same issue than version 2.4.2

  • Version 2.4.2.0 • Released on: 2012-06-27 15:15:55
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    Description:

    Fix: bug encountered when trying to create and bind a SocketServer to an already bound port.

  • Version 2.4.1.0 • Released on: 2012-06-27 15:04:21
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    Description:

    Fix: Deamon.run() becomes synchronous (does not lauch a Thread.bgRun() anymore)

  • Version 2.4.0.0 • Released on: 2012-06-21 13:42:28
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    Description:

    Fix: various bugs

  • Version 0.0.2.0b • Released on: 2012-05-30 09:58:49
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    Description:

    Fix: all the library elements in plugins.ylemontag.matlabio.*, all the common GUI objects in plugins.ylemontag.matlabio.gui.*

  • Version 0.0.1.0b • Released on: 2012-05-25 18:23:08
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