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pr4deepr authored Jun 27, 2024
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# Cellpose
Google Colab notebooks for prediction using cellpose (v2.0).
This currently only supports 2D prediction
**This notebook uses cellpose v2.3.2.**


2D Notebook: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/pr4deepr/cellpose-colab/blob/main/Cellpose_cell_segmentation_2D_prediction_only.ipynb)

Cellpose: Cellpose: https://github.com/MouseLand/cellpose


3D prediction is available by the [ZeroCostDL4Mic team](https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki). The notebooks are inspired by the [ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) series of notebooks from the Henriques Lab and do borrow components from it as well.


v0.3 updates:
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
* Added the new models in the notebook
* Fixed a numpy error when installing cellpose in colab environment. Fix is to restart colab after installing cellpose
* Parameters.txt file gets saved in output folder so as to record the parameters used for cellpose prediction
* 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)

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## Running cellpose and colab on local conda installation
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