diff --git a/README.md b/README.md index 41886709..7a69a498 100644 --- a/README.md +++ b/README.md @@ -20,14 +20,14 @@ A generalist algorithm for cell and nucleus segmentation (v1.0) that can be opti 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). -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: +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: -* [![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) Example google colab notebook for image restoration using new `CellposeDenoiseModel` from Cellpose3 -* [![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) Example google colab notebook with new super-generalist "cyto3" model, try out the new `cyto3` super-generalist Cellpose model with `model_type="cyto3"`. +* [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 +* * [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"`. * [![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) Train your own models with Cellpose. -* [![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) example notebook for Cellpose1 for 2D and 3D segmentation -* [![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) +* [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 +* [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) * [![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) ### CITATION