CellProfiler tutorial pipelines and images
A tutorial that describes building a pipeline to segment the nuclei and cell boundaries of a HeLa cell monolayer in 3d. This tutorial is currently in development.
A tutorial for high-content analysis of imaging flow cytometry (IFC) data with CellProfiler and machine learning can be found here: https://github.com/holgerhennig/machine-learning-IFC
The tutorial is a step by step guide and contains example data, CellProfiler pipelines and a machine learning script (in python) which can serve as a starting point when analyzing your own IFC data.
A tutorial that uses a CellPainting assay to segment organelles and to maximize segmentation robustness.
A tutorial describing how to use ilastik in combination with CellProfiler to segment cells imaged only in phase contrast without any added fluorescence.
A tutorial to show how to use CellProfiler plus CellProfiler Analyst to perform quality control on large scale screens.
A tutorial showing how to segment cells in CellProfiler and then classify them by phenotype in CellProfiler Analyst. This is our standard tutorial for those new to image analysis in general or CellProfiler in particular.
This tutorial from Carolina Wählby, Maxime Bombrun, and Christian Tischer is a great intro to using CellProfiler to find dots per cell.
Neil Anthony from Emory's Integrated Cellular Imaging (ICI) core facility has a number of great image analysis tutorials on YouTube, including a 6-part series on CellProfiler.
