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.

For an introductory tutorial to construct pipelines, visit [YouTube]. CellProfiler: Constructing pipelines. [PDF]

Introductory video tutorials developed by a CellProfiler user can be found on his website page or on [YouTube].

Using CellProfiler and FCS Express 4 Image Cytometry: joint webinar with DeNovo Software on using CellProfiler to peform basic image assays and generate data compatible with export into FCS Express.

For the Imaging Cytometry Flow tutorial, click here

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

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] (relevant example pipelines)

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 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.