Muscle fiber segmentation and muscle fiber type classification with QuPath

This video shows how to segment muscle fibers with Cellpose and how to train an object classifier for each fluorescent marker to identify different fiber types with QuPath. The fluorescence image used in this video showing muscle fibers was acquired at APEX (www6.inrae.fr/....

[@margotissertine2096]

Thank you so much for your videos, it helps me a lot! I just have a question: would it possible to add a line in the code and increase the thickness of the segmentation ? I haven't been able to do so just yet.. If you are open to it, I would love to get in touch with you and discuss it. Thank you so much !

[@thierrypecot8747]

Hi! If you want to expand (dilate) the segmentations, I do not know an easy way to do it, but you can expand annotations. you would have to convert the detections into anotations with a script: def detections = getDetectionObjects() def newAnnotations = detections.collect { return PathObjects.createAnnotationObject(it.getROI(), it.getPathClass()) } removeObjects(detections, true) addObjects(newAnnotations) and then you can expand the annotations by using the command: Objects -> Annotations... Expand annotations. If you just want to visually thicken the segmented objects, I do not know how to do it. Hope this will help!

[@thierrypecot8747]

0:37 Visualization 5:00 Script for segmenting muscle fibers with Cellpose 8:57 Tissue segmentation with thresholder 10:59 Muscle fiber segmentation with Cellpose 16:51 Image duplication for each marker 18:31 Positive and negative annotations for first marker 21:44 Object classifier training for first marker 28:30 Saving object classifier for first marker 29:16 Applying all object classifiers to identify marker(s) associated with each muscle fiber

[@asmaelaouina7047]

your videos are Gold! thank you very much for the hard work!

[@thierrypecot8747]

Glad to see it's helpful!

[@dongxind7646]

Amazing! your videos are very helpful! However, the muscle fibers fluorescence image used in this video cannot open on the website, Can you provide a new download address?😄

[@thierrypecot8747]

Hi! Glad to see it's helpful, unfortunately, this image is not available, sorry.