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README.md

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@@ -23,13 +23,15 @@ Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Ce
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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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* [run_cellpose3.ipynb](https://github.com/MouseLand/cellpose/blob/main/notebooks/run_cellpose3.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](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) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](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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* [run_cyto3.ipynb](https://github.com/MouseLand/cellpose/blob/main/notebooks/run_cellpose3.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](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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* [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](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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* [run_cellpose_GPU.ipynb](https://github.com/MouseLand/cellpose/blob/main/notebooks/run_cellpose_GPU.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](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) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](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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* [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](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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:triangular_flag_on_post: All models in Cellpose, except `yeast_BF_cp3`, `yeast_PhC_cp3`, and `deepbacs_cp3`, are trained on some amount of data that is **CC-BY-NC**. The Cellpose annotated dataset is also CC-BY-NC.
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### CITATION
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**If you use Cellpose 1, 2 or 3, please cite the Cellpose 1.0 [paper](https://t.co/kBMXmPp3Yn?amp=1):**
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**If you use the new image restoration models or cyto3, please also cite the Cellpose3 [paper](https://www.biorxiv.org/content/10.1101/2024.02.10.579780v1):**
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Stringer, C. & Pachitariu, M. (2024). Cellpose3: one-click image restoration for improved segmentation. <em>bioRxiv</em>.
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:triangular_flag_on_post: All models in Cellpose, except `yeast_BF_cp3`, `yeast_PhC_cp3`, and `deepbacs_cp3`, are trained on some amount of data that is **CC-BY-NC**. The Cellpose annotated dataset is also CC-BY-NC.
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### :star2: v3 (Feb 2024) :star2:
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Cellpose3 enables image restoration in the GUI, API and CLI (saved to `_seg.npy`). To learn more...

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