Computer Assisted Segmentation Tool

An AI Based Segmentation Tool For TrakEM2

Outlined cells
Outlined cells
3D representation


The Computer Assisted Segmentation Tool (CAST) is a plugin for TrakEM2. Once it is installed CAST can be found in the TrakEM2 toolbar under the pencil icon. CAST uses a sophisticated machine learning algorithm to differentiate the inside area of a structure from the boundary. This provides the user with the ability to easily outline a given structure with only one click.

Manual Installation:

While downloading the version of Fiji provided here is strongly recommended, the tool can still be installed manually by following these steps. Download the file from below. To install the tool, go to " (Fiji's home directory) > plugins", then delete the file "TrakEM2_-1.0g.jar". Now unzip, copy and paste all three items into " (Fiji's home directory) > plugins". After restarting Fiji the tool should be available in the TrackEM2 toolbar under the pencil icon.

Using CAST

Download Fiji With The Tool Installed


Manual Install Files

Fiji (Windows)

Fiji (Linux)

Fiji (Mac - OS X)

CAST - Verison 1.2

Practice Data

Questions ... Comments

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