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 !

[@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.

[@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!