• Tutorials

    Documents are in PDF and PPS (self-starting Powerpoint slide) format.

    Technical descriptions of CellProfiler and CellProfiler Analyst software can be found in our papers.

    Our introduction to automated image analysis principles and practicalities is published as an educational article at PLoS.

    The NIH has published a introductory chapter  of "best practices" for image-based high-content screening (in which CellProfiler is mentioned) as part of the Assay Guidance Manual,  and our group has published a more advanced follow-up chapter on image analysis methods.

    CellProfiler Video Tutorials

    CellProfiler: Getting Started. Demonstrates some of CellProfiler's features.

    Worm Toolbox. Find individual worms using the Worm Toolbox

    Pipeline example to find individual worms. [PDF]
    For the worm toolbox tutorial, click here

    CellProfiler Written Tutorials

    • We also post guided exercises as part of our educational outreach effort here.

    CellProfiler Analyst Video Tutorials

    Demonstrates some of CellProfiler Analyst's data exploration features. [PDF]
    Provides an example of selecting phenotypes using gating.
    For applying the machine learning tool to identify a phenotype of interest, watch this tutorial [youtube].
    Classifying cells with machine learning [PDF]
    For all CellProfiler tutorials, visit our YouTube channel.