Tutorials

Movies are in Quicktime format. Get the Quicktime plugin.
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

• Getting started with CellProfiler (3 min 51 sec, 27MB .mov). Demonstrates some of CellProfiler's features.
• Constructing pipelines (8 min 41 sec, 75MB .mov). Provides an introductory tutorial to constructing pipelines.
• Using CellProfiler and FCS Express Image Cytometry (63 min, 88MB .wmv). Joint webinar with DeNovo Software on using CellProfiler to peform basic image assays and generate data compatible with export into FCS Express.


• Selecting a thresholding method (coming soon)
• Correction factors and upper/lower limits (coming soon)
• Segmentation and declumping methods (coming soon)
• Smoothing filter and maxima size selection (coming soon)
• Filtering primary objects (coming soon)

CellProfiler Written Tutorials

• Getting started with CellProfiler [PPS] (file runs in "play-presentation" mode when double-clicked)
• 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)

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

CellProfiler Analyst Video Tutorials

• Exploring image data (5 min 30 sec, 33MB .mov). Demonstrates some of CellProfiler Analyst's data exploration features.
• Scoring cell populations (3 min 30 sec, 23MB .mov). Provides an example of selecting phenotypes using gating.
• Classifying cells with machine learning (7 mins 38.5MB .mov). Shows how to apply the machine learning tool to identify a phenotype of interest.