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MLB
26 Jul 2013 11:26
Thanks ! It helps.

Matlab X server

by Yoann Le Montagner

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.

Publication Id
ICY-X5I8R9
See technical details
View complete changelog

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 http://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)