Workflow Demos

BioImageFlow’s example workflows are executable demos. Each page below introduces a real analysis pattern, names the data source, shows the default command, and describes the files produced by the run.

The examples are deliberately scoped so the graph can be read and adapted, while the real-data paths point to established microscopy data sources such as the Cell Image Library, BBBC038, and the Cell Tracking Challenge.

• FISH Spot Counting Per Nucleus
• Exploring ATLAS Spot Detection Parameters
• Benchmarking Nuclei Segmentation on BBBC038
• Cell Counting and Phenotyping
• Low-SNR Restoration
• SAIRPICO Deconvolution
• Live-Cell Migration Tracking

Start with FISH Spot Counting Per Nucleus for the most complete end-to-end example. The remaining pages cover spot-detection parameter sweeps, segmentation benchmarking, object measurement, restoration, deconvolution, and migration tracking.