A035 - Cellpose 2.0 and TrackMate: A powerful combination for effortless and accurate analysis of live cells in phase microscopy

Alexandre Hego (alexandre.hego@uliege.be)
Rémy Flores-flores (remy.flores-flores@inserm.fr)

The analysis of live cells using phase microscopy is a crucial tool in the field of cell biology, but conventional methods of segmentation can be prone to errors. Many researchers use phase microscopy like the Incucyte microscope from Sartorius. This workshop will be particularly useful for those who are using this type of microscope, as it will provide them with the tools to analyze the data more efficiently and accurately. In this workshop, we will introduce participants to Cellpose 2.0, an AI-based tool for the accurate segmentation of live cells in phase microscopy images. Cellpose 2.0 offers a user-friendly graphic user interface (GUI) that makes it easy for researchers to predict the results and retrain the model using a human-in-the-loop method. The workshop will cover the basics of using Cellpose 2.0, including installation of the GUI, loading and predicting images, and retraining the model using their own data. In addition to the Cellpose 2.0 GUI, the workshop will also introduce two other tools available in Fiji. First, the BIOP Cellpose wrapper, which allows the use of a working Cellpose environment from Fiji and is an easy and convenient tool for scripting in ImageJ macro for batch prediction of Cellpose. Second, TrackMate, a powerful plugin for tracking cells in microscopy images that is distributed in Fiji. Participants will have the opportunity to work with all the tools on their own datasets and gain hands-on experience with the software. This will enable them to analyze live cell imaging data and improve their research efficiently and accurately.