diff --git a/README.md b/README.md index 66f19dbb..006b8f8f 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,31 @@ [![Build Status](https://github.com/trackmate-sc/TrackMate-Cellpose/actions/workflows/build.yml/badge.svg)](https://github.com/trackmate-sc/TrackMate-Cellpose/actions/workflows/build.yml) -# cellpose and omnipose ntegration in TrackMate. +# Omnipose integration in TrackMate. -cellpose and omnipose integration in TrackMate +The Omnipose integration in TrackMate works roughly as the Cellpose integration one. +It requires Omnipose to be installed on your system and working independently. This page gives installation details and advices at how to use the omnipose integration in TrackMate. -## omnipose +## Omnipose +Omnipose is a segmentation algorithm based on Deep-Learning techniques, and inspired from the Cellpose architecture. Omnipose is well suited for bacterial cell segmentation, and achieves remarkable performances on mixed bacterial cultures, antibiotic-treated cells and cells of elongated or branched morphology. -### Example +If you use the Omnipose TrackMate module for your research, please also cite the Omnipose paper: +[Cutler, K.J., Stringer, C., Lo, T.W. et al. Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation. Nat Methods 19, 1438–1448 (2022)](https://www.nature.com/articles/s41592-022-01639-4). + + + +## Example https://github.com/marieanselmet/TrackMate-Omnipose/assets/32811540/3c2365c9-8d1b-4057-b4d1-2939e4e2b818 -*Time-lapse captured by Rodrigo Arias Cartin, Frédéric Barras lab, Institut Pasteur* +*E. Coli, Marie Anselmet and Rodrigo Arias Cartin, Barras lab, Institut Pasteur* + + +## Omnipose installation +This code works with the Omnipose version 0.3.6. It doesn't work with the last version of Omnipose. -### Version -This code works with the Omnipose version 0.3.6. It doesn't work with the last version of Omnipose (same issue as for the [Omnipose utility wrapper of the BIOP](https://github.com/BIOP/ijl-utilities-wrappers)). +To install Omnipose, you can refer directly to the installation guide provided on the [Omnipose repository](https://github.com/kevinjohncutler/omnipose#how-to-install-omnipose). -I set my Windows installation as follows, to work on GPU: +An example Windows installation working on GPU: ``` conda create -n omnipose conda activate omnipose @@ -24,4 +34,4 @@ pip install omnipose==0.3.6 pip install cellpose-omni==0.7.3 ``` -The default model *bact_phase_omni* is stored in cellpose pretrained models folder. +The default models *bact_phase_omni* and *bact_fluor_omni* are stored in the cellpose pretrained models folder.