CellProfiler Video Tutorials


Visit our YouTube playlist for video tutorials on CellProfiler, CellProfiler Analyst, segmentation strategies, how to construct pipelines, and much more.

CellProfiler Written Tutorials

Technical descriptions of CellProfiler and CellProfiler Analyst software can be found in our papers while more written tutorials can be found on the CellProfiler GitHub page. 

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.

Using CellProfiler for Quantitative Image Analysis [PPT]

Using the Input modules in CellProfiler 2.1:

  • Images [PDF]
  • Metadata [PDF]
  • NamesAndTypes [PDF]
  • Groups [PDF]
  • Loading image stacks and movies [PDF]

Identifying, measuring, and classifying yeast colonies [PDF] (relevant example pipeline)

Identifying and measuring cells: Cytoplasm-nucleus translocation assay [PDF] (relevant example pipeline)

Calculating and applying illumination correction for images [PDF] (relevant example pipeline)

Using the Worm Toolbox for image analysis of C. elegans phenotypes [PDF]

Performing a colocalization assay [PDF] (relevant example pipeline)

Simple nuclei identification tutorial [PDF] (sample data) (courtesy of the German BioImaging network)

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