This notebook uses cellpose v2.3.2.
2D Notebook:
Please cite the following, if you use this notebook:
- Cellpose: Stringer, C., Wang, T., Michaelos, M. et al. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021). https://doi.org/10.1038/s41592-020-01018-x
- Pradeep Rajasekhar. (2025). Cellpose Google Colab segmentation notebook (v0.6). Zenodo. https://doi.org/10.5281/zenodo.15073575
Change version number for notebook based on what you've used
Cellpose: Cellpose: https://github.com/MouseLand/cellpose
3D prediction is available by the ZeroCostDL4Mic team. The notebooks are inspired by the ZeroCostDL4Mic series of notebooks from the Henriques Lab and do borrow components from it as well.
v0.6 update:
- Fixed numpy bug by restricting it to numpy<2
- Added uv for fast python package installation
v0.5 update:
- 2024/04/09 Constrained cellpose version to be 2.3.2 to maintain compatibility.
v0.4 update:
- Fixed bug where new models could not be used for prediction
v0.3 update:
- Updated for Cellpose 2.0
- New models incorporated: https://cellpose.readthedocs.io/en/latest/models.html
- Parameters used in cellpose will be saved as a txt file (Thanks for suggestion Kota Miura)
This is mainly if you'd like to train data using your PC resources Installation instructions are provided in the notebook below. The cellpose_colab_local.yml file provided here is only for upgrading the existing cellpose environment. Check the notebook below for more info.
2D Notebook_local_environment (run locally on a PC):
This is not guaranteed to work on every system. If you have an error:
ImportError: Numba needs NumPy 1.21 or less
Run:
pip install numpy==1.21