Tutorials

CellProfiler tutorial pipelines and images

Generate Convert Improve

Install / Use

/learn @CellProfiler/Tutorials

About this skill

Quality Score

0/100

README

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.

auto-gen TOC: {:toc}

Beginner 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.

Versión en español:

Versão em português:

Bonus materials

We have also created bonus materials designed to go with this tutorial - in these exercises, you will practice using CellProfiler to interface with other software tools like ilastik and Cellpose and in doing so will learn how to use CellProfiler plugins.

English version <a href="https://github.com/CellProfiler/tutorials/raw/master/BeginnerSegmentation/bonus_materials_EN.zip" target="_blank"><img src="assets/img/download-button.png" alt="Download button" width="140px"></a>

Versión en Español <a href="https://github.com/CellProfiler/tutorials/raw/master/BeginnerSegmentation/bonus_materials_ES.zip" target="_blank"><img src="assets/img/download-button.png" alt="Download button" width="140px"></a>

Versão em português: <a href="https://github.com/CellProfiler/tutorials/raw/master/BeginnerSegmentation/bonus_materials_PT.zip" target="_blank"><img src="assets/img/download-button.png" alt="Download button" width="140px"></a>

Advanced 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.

En español:

Translocation

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.

En español:

3D segmentation of cell monolayer

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.

En español:

Pixel-based Classification

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

Quality Control

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

Annotation

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.

Input Modules

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.

3D Noise Nuclei segmentation

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

3D FISH in C. elegans 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.

UnmixColors Tutorial

A tutorial that describes how to use the UnmixColors module.

<a href="https://www.youtube.com/watch?v

Related Skills

node-connect

343.1k

Diagnose OpenClaw node connection and pairing failures for Android, iOS, and macOS companion apps

frontend-design

90.0k

Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, or applications. Generates creative, polished code that avoids generic AI aesthetics.

openai-whisper-api

343.1k

Transcribe audio via OpenAI Audio Transcriptions API (Whisper).

qqbot-media

343.1k

QQBot 富媒体收发能力。使用 <qqmedia> 标签，系统根据文件扩展名自动识别类型（图片/语音/视频/文件）。