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 an introductory tutorial to construct pipelines, visit [YouTube]. CellProfiler: Constructing pipelines . [PDF]
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- Using CellProfiler and FCS Express 4 Image Cytometry: joint webinar withDeNovo Software on using CellProfiler to peform basic image assays and generate data compatible with export into FCS Express.
CellProfiler Written Tutorials
- Using CellProfiler for Quantitative Image Analysis[PPT]
- Using the Input modules in CellProfiler 2.1:
- 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 theWorm Toolbox for image analysis ofC. elegans phenotypes[PDF] (relevant example pipelines)
- Performing a colocalization assay[PDF] (relevant example pipeline)
- Simple nuclei identification tutorial[PDF] (sample data) (courtesy of theGerman BioImaging network)
- We also post guided exercises as part of our educational outreach efforthere.
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.
For the worm toolbox tutorial, click here
For the Imaging Cytometry Flow tutorial, click here