Code used to enhance image analysis of influenza viral RNA
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This directory contains matlab scripts that can be used as XTension plugins with the image processing software Imaris from BitPlane. The following scripts are useful for finding colocalized spots across multiple microscopy channels in images obtained from techniques such as fluorescence in-situ hybridization (FISH). Feel free to use these scripts in your analysis and modify them as needed.

To use these extensions for analysis of images, simply copy the '.m' files into your Imaris MATLAB XTensions directory. In Windows, this is usually found under

C:\Program Files\Bitplane\Imaris x64 8.4.1\XT\matlab\

or replace 'C:\Program Files\Bitplane\Imaris x64 8.4.1' with the directory in which you can find your Imaris installation.

Once copied, restart Imaris, or under Preferences>CustomTools>Xtension Folders, re-choose the above mentioned directory and the new scripts will show up under "Tools" . For example, the XTSpotsColocalizeFISH.m will appear under "Tools", denoted by the pink cog, when a "Spots" object is selected and under Image Processing>Spots Functions.

A detailed explanation of what each script does can be found in the comments at the beginning of each script file. In brief, here is what the following files do:

Filename function
XTSpotsColocalizeFISH.m finds colocalized spots from a collection of up to 3 spot objects.
XTSpotsColocalizeFISH4.m finds colocalized spots from a collection of up to 4 spot objects.
XTExportSpotsXLS.m export spot and track information from a time-resolved Imaris dataset
XTTrackConnectStartAndEnd.m identify split/merge locations and make missing connections in Imaris
node_network_analysis.m use XLS file exported by XTExportSpotsXLS.m to analyse as a directed graph in MATLAB