305 - What is Cellpose algorithm for segmentation?

What is Cellpose algorithm for instance segmentation? and how to train your own Cellpose model?

Code generated in the video can be downloaded from here:

All other code:

Useful links:

Cellpose is a generalist algorithm for cellular segmentation which can very precisely segment a wide range of image types out of-the-box and does not require model retraining or parameter adjustments.

This video demonstrates the use of Cellpose in Google Colab on a custom data set.

[yujanshrestha]

Another great presentation. I find it fascinating that reformulating the output from a binary mask to flows results in such performance. Do you think this yields any insight on how (or what) the U-net learns?

[damanrique]

Hi Sreeni. I have advanced a lot in my research thanks to your insightful videos. I keep having problems with segmentation. Algorithms like cellpose or others you have explored in the channel work very well for circular or oval objects, or for those that border each other. I study glial cells in the brain, objects that are highly irregular, branching, and strongly overlapping with each other. It would be great if you could explore some object segmentation and identification algorithms for those cases. Greetings from Canada

[awaisahmad]

Thank You Alot. You are the best teacher.

[efuaewusi-brown]

Can Cellpose segment and number cells in order from multiple similar images (obtained from different stainings of same sections)

[Dina-scks]

Hello 👋! Thank you for video 😊, all your videos are very helpful❤. Could you help me, I need to choose best PC for machine learning especially for segmentation task

[urzdvd]

Hi Sreeni, great great video thanks a lot, I'm going to use this model to my pap smear dataset, right now with stardist I have decent results but not great in segmenting multiclass, do you recomend another model?, so far I have good results in the Apeer Zeiss but unfortunately the model is closed and I cannot see the strecture used.

[emmanuelailok]

Hi Sreeni! Thanks fo the video! I am currently a high school student doing research on cervical cancer and I am evaluating the performance of cervical cancer classification systems specifically using handcrafted features vs CNN features. For the handcrafted features, I am having issues with my code and would like to ask whether you could be of help in that. I can share my linkedln/email if needed. I would really appreciate it thank you!

[ribwarjahani]

Hello, did you mention changing the Python version in Google Collab in your training? Thank you if there is a way to do this
For example, changing the current version 3.10.6 to 3.6

[dounia]

Hello sir please I need the code for unmasking face by gan network