This pipeline demonstrates the analysis of objects that are aligned (or "stitched") in a form of a grid (or montage). This is typically seen in downstream analysis of Imaging flow cytometry, where hundred thousands of images of single cells are collected and stitched together in a montage.

In this pipeline, we identify objects based on the brightfield signals, in an attempt to quantify cellular features in label-free experiments.

See more Imaging flow cytometry data analysis at: http://cellprofiler.org/imagingflowcytometry/

Open-source stitching script (python) can be downloaded at: https://github.com/CellProfiler/stitching