Using Cellpose and StarDist in CellProfiler

In this tutorial, we will demonstrate how to use new CellProfiler plugins for deep learning-based segmentation with Cellpose and StarDist. The Cellpose and StarDist algorithms robustly identify diverse cell types. The plugins we will discuss (RunCellpose and RunStardist) make these algorithms more accessible and allow for their inclusion in existing CellProfiler workflows. We will demonstrate how to use RunCellpose and RunStardist to analyze 2D and 3D image sets. Links: Download CellProfiler plugins: https://github.com/CellProfiler/CellP... Instructions on installing runCellpose and runStarDist plugins: https://github.com/CellProfiler/CellP... CellProfiler Wiki (with instructions for how to install CellProfiler from source): https://github.com/CellProfiler/CellP... A few tips: RunStarDist is generally faster and since it assumes star-convex shapes, is best suited for nuclei or roundish cells. RunCellpose and the Omnipose models within are a good starting point for segmenting non-convex cells. For either tool, a GPU will help increase speed/efficiency dramatically. This tutorial assumes participants are already familiar with using CellProfiler.