Update README.md

Adding docu in the README

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.