VolumeAnnotationBot

A bot and tool to annotate 3D volumes.

Usage: call 'volumeAnnotationBot' and follow the instructions.
This bot requires the bfmatlab toolbox to read stacks.
Download here: http://downloads.openmicroscopy.org/bio-formats/5.3.4/
Label masks are saved in the same folder as the volume.
If you already have a double, range [0,1] 3D volume loaded into Matlab,
call volumeAnnotationTool as in the example below.
load mri
V = double(squeeze(D))/255;
VAT = volumeAnnotationTool(V,2); % the second parameter is the number of labels
The label masks can then be accessed at VAT.LabelMasks

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MatBots are primitive AIs, 'assistants' if you will, that use minimalistic GUI dialogs to guide the user through a data processing pipeline in Matlab.

Isn't that an 'app'? Bots are much more restrictive than apps. Users are, to a greater extent than in an app, guided through the correct steps to perform a task. A bot usually performs a much more limited task than an app.

When possible, bots have a 'headless' mode, which allows them to execute a processing pipeline as a typical Matlab function, either on an image or a folder of images.

For more bots and tools, see https://hms-idac.github.io/MatBots/