Cell segmentation

This workflow applies a Stardist pre-trained model (versatile_fluo or versatile_HE) depending on the input images ie. uses both models for a dataset including both fluorescence (grayscale or RGB where all channels are equal) and H&E stained (RGB where channels are not equal) images.

This version uses tensorflow CPU version (See Dockerfile) to ensure compatibility with a larger number of computers. A GPU version should be possible by adapting the Dockerfile with tensorflow-gpu and/or nvidia-docker images.

This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It performs 2D nuclei segmentation using pre-trained nuclei segmentation models of Cellpose. And it was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

The Incucyte® Base Analysis Software provides a guided interface and purpose-built tools, which include the process of acquiring, viewing, analyzing and sharing images of living cells.

The authors present an ImageJ-based, semi-automated phagocytosis workflow to rapidly quantitate three distinct stages during the early engulfment of opsonized beads.