Computer Assisted Segmentation Tool

Description:

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 CAST.zip file from below. To install the tool, go to "Fiji.app (Fiji's home directory) > plugins", then delete the file "TrakEM2_-1.0g.jar". Now unzip CAST.zip, copy and paste all three items into "Fiji.app (Fiji's home directory) > plugins". After restarting Fiji the tool should be available in the TrackEM2 toolbar under the pencil icon.

Using CAST

• The tool is located in the toolbar under the pencil icon.
• Once the pencil icon is selected, a box appears.
• To increase or decrease the size of the selection box press and hold shift while moving the scroll wheel on the mouse.
• To set boundary padding for leak control, increase the number in boundary padding box under the “tool options” panel.
• Once the box is the desired size and all of the settings are satisfactory, left click the mouse to start tracing. The algorithm will concentrate on the structure surrounding the click point.
• Once the mouse is clicked the image inside the box will be fed into the neural network, and a classified image will be created. The expand area algorithm will then analyze the classified image and populate the arealist.