FIJI (ImageJ): Trainable Weka Segmentation [Segmenting RGB and Low-Contrast Images]

Learn how to use FIJI (ImageJ) to segment RGB (color or monochromatic) images, brightfield and other low-contrast images using the FIJI plugin Trainable Weka Segmentation. This plugin combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations or classifications of biological or non-biological images.
Image credits:
Khaled Hamza
Lukáš Rausa (MTF STU v Trnave)
Plugin citation: Arganda-Carreras, I., Kaynig, V., Rueden, C., Eliceiri, K. W., Schindelin, J., Cardona, A., & Sebastian Seung, H. (2017). Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics, 33(15), 2424-2426. doi:10.1093/bioinformatics/btx180
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[@PLTC7162]

Kudos for making these excellent videos. However: (1) the cursor speed is "supersonic" - the viewer has to slow down the speed to 0.5 or even 0.25 to be able to follow it; (2) moving the cursor back and forth over menu items you are not going to select is confusing and a waste of time - please go directly to the items you will use and only to those items; similarly, avoid hovering over regions of the image - without text, it is unclear why you are doing that; (3) the music is intrusive and distracts the viewer - either replace it with softer background music or remove it.
Thank you

[@johanna.m.dela-cruz]

@PLTC7162 Thanks, I appreciate the time you took to share your feedback.

[@shuowang5674]

Your instruction is fantastic~ I have a question: I could right-click on classes 1 and 2 to set their colors, but I couldn’t set colors for other classes by right-clicking. Could anyone help me out? Thanks a lot!

[@johanna.m.dela-cruz]

Hi @shuowang5674. Thanks for watching. Unfortunately, setting colors for new classes isn't part of the current set up for TWS (unless I'm missing something). As soon as you 'create result', you can change the colors of the label image that is generated. You can use MorphoLibJ to set a label map - this can give you other colors representing your different classes.

[@林崇智-c2x]

can you tell me how to use gpu-based weka 3d segmetation? thank you

[@johanna.m.dela-cruz]

Hello. Other than in Fiji, I have not tried weka. You might want to go to the main weka website at www.cs.waikato.ac.nz/ml/weka/.