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.
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
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/
Plane views in independent windows for easier annotation.
Download apps, toolboxes, and other File Exchange content using Add-On Explorer in MATLAB.