cellpose 2.0 tutorial: how to train your own cellular segmentation model

Generalist models for cellular segmentation, like Cellpose, provide good out-of-the-box results for many types of images. However, such models do not allow users to adapt the segmentation style to their specific needs and may perform sub-optimally for test images that are very different from the training images. Here we introduce Cellpose 2.0, a new package which includes an ensemble of diverse pretrained models as well as a human-in-the-loop pipeline for quickly prototyping new specialist models. We show that specialist models pretrained on the Cellpose dataset can achieve state-of-the-art segmentation on new image categories with very little user-provided training data. Models trained on 500-1000 segmented regions-of-interest (ROIs) performed nearly as well as models trained on entire datasets with up to 200,000 ROIs. A human-in-the-loop approach further reduced the required user annotations to 100-200 ROIs, while maintaining state-of-the-art segmentation performance. This approach enables a new generation of specialist segmentation models that can be trained on new image types with only 1-2 hours of user effort. We provide software tools including an annotation GUI, a model zoo and a human-in-the-loop pipeline to facilitate the adoption of Cellpose 2.0.

In this tutorial we go through how the annotation GUI works, how to train your own model in the GUI, and how to train and use custom models in google colab or your own local jupyter notebook / python script.

Paper: https://www.biorxiv.org/content/10.11...
Code: https://github.com/MouseLand/cellpose
Slides: https://docs.google.com/presentation/...
Notebook: https://colab.research.google.com/git...