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@@ -20,14 +20,14 @@ A generalist algorithm for cell and nucleus segmentation (v1.0) that can be opti
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Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Cellpose3 (image restoration), read the [paper](https://www.biorxiv.org/content/10.1101/2024.02.10.579780v1). To learn about Cellpose 2.0 (human-in-the-loop), read the [paper](https://www.nature.com/articles/s41592-022-01663-4) or watch the [talk](https://www.youtube.com/watch?v=3ydtAhfq6H0). To learn about Cellpose 1.0, read the [paper](https://t.co/kBMXmPp3Yn?amp=1) or watch the [talk](https://t.co/JChCsTD0SK?amp=1). For support, please open an [issue](https://github.com/MouseLand/cellpose/issues).
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Please see install instructions [below](README.md/#Installation), and also check out the detailed documentation at [**cellpose.readthedocs.io**](https://cellpose.readthedocs.io/en/latest/) for more information. Example notebooks in colab for install-free option:
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Please see install instructions [below](README.md/#Installation), and also check out the detailed documentation at [**cellpose.readthedocs.io**](https://cellpose.readthedocs.io/en/latest/) for more information. Example notebooks:
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*[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cellpose3.ipynb)Example google colab notebook for image restoration using new `CellposeDenoiseModel` from Cellpose3
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*[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cyto3.ipynb)Example google colab notebook with new super-generalist "cyto3" model, try out the new `cyto3` super-generalist Cellpose model with `model_type="cyto3"`.
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*[run_cellpose3.ipynb](https://github.com/MouseLand/cellpose/blob/main/notebooks/run_cellpose3.ipynb)[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cellpose3.ipynb)shows how to run image restoration using new `CellposeDenoiseModel` from Cellpose3
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**[run_cyto3.ipynb](https://github.com/MouseLand/cellpose/blob/main/notebooks/run_cellpose3.ipynb)[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cyto3.ipynb)shows how to use new super-generalist "cyto3" model with `model_type="cyto3"`.
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*[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cellpose_2.ipynb)
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Train your own models with Cellpose.
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*[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cellpose_GPU.ipynb)example notebook for Cellpose1 for 2D and 3D segmentation
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*[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/Cellpose_cell_segmentation_2D_prediction_only.ipynb) a user-friendly notebook for 2D segmentation written by [@pr4deepr](https://github.com/pr4deepr)
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*[run_cellpose_GPU.ipynb](https://github.com/MouseLand/cellpose/blob/main/notebooks/run_cellpose_GPU.ipynb)[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/run_cellpose_GPU.ipynb)runs Cellpose segmentation in 2D and 3D
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*[Cellpose_cell_segmentation_2D_prediction_only.ipynb](https://github.com/MouseLand/cellpose/blob/main/notebooks/Cellpose_cell_segmentation_2D_prediction_only.ipynb)[](https://colab.research.google.com/github/MouseLand/cellpose/blob/main/notebooks/Cellpose_cell_segmentation_2D_prediction_only.ipynb) a user-friendly notebook for 2D segmentation written by [@pr4deepr](https://github.com/pr4deepr)
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*[](https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/Beta%20notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb) a user-friendly [ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic) notebook that includes training cellpose models, written by [@guijacquemet](https://github.com/guijacquemet)
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