Skip to content

Commit

Permalink
Update README.md
Browse files Browse the repository at this point in the history
  • Loading branch information
carsen-stringer committed Feb 14, 2024
1 parent ffbf8d0 commit e3f6eb7
Showing 1 changed file with 10 additions and 11 deletions.
21 changes: 10 additions & 11 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,20 @@
[![GitHub stars](https://img.shields.io/github/stars/MouseLand/cellpose?style=social)](https://github.com/MouseLand/cellpose/)
[![GitHub forks](https://img.shields.io/github/forks/MouseLand/cellpose?style=social)](https://github.com/MouseLand/cellpose/)

A generalist algorithm for cell and nucleus segmentation (v1.0) that can be optimized for your own data (v2.0).

Cellpose was written by Carsen Stringer and Marius Pachitariu. 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).
A generalist algorithm for cell and nucleus segmentation (v1.0) that can be optimized for your own data (v2.0) and (**NEW**) perform image restoration (v3.0).

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.

### :star2: v3 (Feb 2024) :star2:

Cellpose3 enables image restoration in the GUI and the API (CLI support and example notebooks coming soon!) To learn more...
* Check out the paper [thread](https://neuromatch.social/@computingnature/111932247922392030).
* Check out the [paper](https://www.biorxiv.org/content/10.1101/2024.02.10.579780v1).

Try out the new `cyto3` super-generalist Cellpose model with `model_type="cyto3"`. There are some Cellpose API changes from v2.0 which will be documented soon.

### CITATION

**If you use Cellpose 1 or 2, please cite the Cellpose 1.0 [paper](https://t.co/kBMXmPp3Yn?amp=1):**
Expand All @@ -36,14 +43,6 @@ Stringer, C. & Pachitariu, M. (2024). Cellpose3: one-click image restoration for

: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.

### :star2: v3 (Feb 2024) :star2:

Cellpose3 enables image restoration in the GUI and the API (CLI support and example notebooks coming soon!) To learn more...
* Check out the paper [thread]().
* Check out the [paper](https://www.biorxiv.org/content/10.1101/2024.02.10.579780v1).

Try out the new `cyto3` super-generalist Cellpose model with `model_type="cyto3"`. There are some Cellpose API changes from v2.0 which will be documented soon.

### :star2: v2.0 (April 2022) :star2:

Cellpose 2.0 now allows human-in-the-loop training of models! To learn more...
Expand Down

0 comments on commit e3f6eb7

Please sign in to comment.