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: Getting Started. Demonstrates some of CellProfiler’s features.
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
Using CellProfiler for Quantitative Image Analysis [PPT]
We also post guided exercises as part of our educational outreach effort here.
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.