FIJI (ImageJ): Trainable Weka Segmentation 3D [Working with Image Stacks or Sequences]

Learn how to use FIJI (ImageJ) to segment image stacks or sequences using the plugin Trainable Weka Segmentation (TWS) 3D.
TWS documentation:
Ignacio Arganda-Carreras, Verena Kaynig, Curtis Rueden, Kevin W Eliceiri, Johannes Schindelin, Albert Cardona, H Sebastian Seung, Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification, Bioinformatics, Volume 33, Issue 15, 01 August 2017, Pages 2424-2426, doi.org/10.1093/bioinformatic...
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[@yangchaod1553]

Many thanks! Really helpful

[@danieljohnson1885]

Hello @johanna.m.dela-cruz , thank you for this tutorial. When I follow your steps and try to apply my saved classifier to an image stack, I get the error "*filename.png* is a 2D image and Weka is working in 3D. However, I tell it to process my entire image sequence, which together form a 3D image. What is your filetype, it looks like you only select one file, but there are somehow 10 images within it? There doesn't appear to be any way to save an image sequence as one file, so far as I can tell. Any advice?

[@johanna.m.dela-cruz]

Hi @danieljohnson1885. You might have to open your image sequence first as a stack. The stack should be made up of all the images in your folder. Here’s a demo: m.th-cam.com/video/_D1kbKjZtjk/w-d-xo.html. Start at @0:58 of this video - no need to check ‘use as virtual stack’.

[@christianburns1658]

Could you show how to use LabKit?

[@johanna.m.dela-cruz]

@christianburns1658. Hi Christian. Although I haven’t tried LabKit yet, I will learn it and share what I have learned with my followers. Thanks for the suggestion.

[@karlyoung5089]

my! l