Introduction to tutorials

CellProfiler tutorials are exercises we’ve guided groups of users through to help them better understand how to use CellProfiler. Please also check out our examples page, which includes additional pipelines and materials for using CellProfiler with specific samples and imaging applications.

Translocation

example segmentation

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.

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Beginner Segmentation

example segmentation

A tutorial that uses a CellPainting assay to find segmentation parameters for larger “parent” objects (nucleus, cell, and cytoplasm) and show you ways to pull out smaller features in your image by segmenting organelles within the nuclei. You will also be shown how to use RelateObjects so that you can relate the average counts, distances, and measurements of the smaller “child” organelles to their larger “parent” objects.

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Advanced Segmentation

example segmentation

This exercise will guide you through setting segmentation parameters that will be robust across your sample. Additionally, it will show you some ways to pull out smaller features in your image by segmenting organelles within the cells and nuclei. You will learn how to use RelateObjects module to obtain average counts, distances, and measurements of the smaller organelles inside their larger parent objects.

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3D segmentation of cell monolayer

example segmentation

A tutorial that describes building a pipeline to segment the nuclei and cell boundaries of a HeLa cell monolayer in 3d using the Watershed module.

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Pixel-based Classification

example segmentation

A tutorial describing how to use ilastik in combination with CellProfiler to segment cells imaged only in phase contrast without any added fluorescence.

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Quality Control

example segmentation

A tutorial to show how to use CellProfiler plus CellProfiler Analyst to perform quality control on large scale screens.

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Annotation

example segmentation

A tutorial to outlines a method for annotating image data using CellProfiler together with another open source software, GIMP. This method is best for annotating or labeling objects to define their boundaries, exactly, as opposed to annotating an image with bounding boxes or centroids.

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Input Modules

example segmentation

A tutorial to introduce you to four modules in CellProfiler; Images, Metadata, NamesAndTypes, and Groups (collectively known as the Input modules). These modules are crucial for any CellProfiler pipeline because they define how images are loaded and organized in CellProfiler for downstream analysis.

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3D Noise Nuclei segmentation

example segmentation

A tutorial that describes building a pipeline to segment the nuclei boundaries in noise 3d images using the ReduceNoise and IdentifyPrimaryObjects modules.

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3D FISH in C. elegans segmentation

example segmentation

A tutorial that describes building a pipeline to segment spots (FISH staining) on C. elegans worms in noise 3d images using background subtraction and Watershed module.

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UnmixColors Tutorial

example segmentation

A tutorial that describes how to use the UnmixColors module.

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Other video tutorials

See more video tutorials on the Center for Open Bioimage Analysis (COBA) YouTube account


Tutorials for image-based profiling

Introduction to morphological profiling

example graphs

A tutorial that introduces the concepts behind image-based profiling (aka morphological profiling), which allows you to extract additional and potentially unforseen biological insights from your image data

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Normalization

figures

A blog post on normalizing Cell Painting data for use in image-based profiling.

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Tutorials for older versions of CellProfiler

ImagingFlowCytometry

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.

Spot counting for beginners

This tutorial from Carolina Wählby, Maxime Bombrun, and Christian Tischer is a great intro to using CellProfiler to find dots per cell.

YouTube Tutorials

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.