So you’re a biologist interested in Cell Painting and don’t know where to get started? We’ve got you covered! For each question below, we’ve arranged the resources in increasing order of detail and/or specificity, so you may find that you don’t need to interact with every resource to glean the information you need.

What is Cell Painting?

• Start by watching AskErinDearBeth Episode 23 - Introduction to the Cell Painting Assay for a casual podcast introduction.
• Read the introduction in the most recent Cell Painting Protocol paper

What can Cell Painting do?

• Read the recent review Cell Painting: a decade of discovery and innovation in cellular imaging
• Read a prior review Image-based profiling for drug discovery: due for a machine-learning upgrade?
• Check out talks on Youtube playlists from Anne Carpenter (https://broad.io/CarpenterVideos) and Shantanu Singh (https://broad.io/SinghVideos)

I’d like to modify the Cell Painting Assay. Can I do that?

You sure can! The Cell Painting Assay is very robust to changes.

• Start by watching Ask Erin Dear Beth Episode Episode 30: Modifying the Cell Painting Assay for a casual podcast introduction.
• Read the most recent Cell Painting Protocol paper for quantification of how modifications affect the strength of the assay and Assessing the performance of the Cell Painting assay across different imaging systems for further modifications related to the microscopes themselves.
• Look in the Cell Painting wiki for some of the modifications that were tested in the development of the Cell Painting Assay.
• The Cell Painting Gallery hosts a LOT of Cell Painting data. You can find many examples of published datasets using a variety of modified Cell Painting protocols in the Cell Painting Gallery.

How do I perform my own image analysis on a batch of Cell Painting images?

• If you don’t already have a strong background in quantitative bioimaging, read the Bioimaging Guide and its companion publication for background information. Watch Ask Erin Dear Beth Episode 20 - Intro to the Bioimaging Guide for a podcast introduction.
• The most recent Cell Painting Protocol paper includes the image analysis workflow.
• The Image Based Profiling Handbook is a step-by-step protocol using a specific tech stack (Distributed-CellProfiler on AWS on images generated by a PerkinElmer microscope, then collating the data with cytominer-database and analyzing it with pycytominer) but the basic procedure for running a Cell Painting experiment is the same no matter the microscope or the processing platform.
• An assortment of Cell Painting pipelines for CellProfiler (tuned for different cell types and microscope parameters) are available in this repository. The current standard pipelines on which we build all our pipelines currently are in JUMP Production pipelines.
• Watch a video walkthrough of the JUMP Production CellProfiler analysis pipeline.
• Watch Ask Erin Dear Beth Episode 3 - QC on High Content Imaging Datasets using CellProfiler and Fiji for details on our QC step in the Cell Painting Assay
• Watch Ask Erin Dear Beth Episode 14 - Illumination Correction in CellProfiler (Two Ways!) for details on the illumination correction we perform in the Cell Painting Assay
• Read the blog post When to Say Good Enough to decide when to stop trying to tune your pipelines!
• Understand all of the nitty gritty details of how we structure all of the data in a Cell Painting dataset by reading Data Structure in the Cell Painting Gallery.

I’ve done image analysis and extracted image features. How do I make profiles?

• Read the blog post How to Normalize Cell Painting Data
• For a big picture overview, read the paper Data-analysis strategies for image-based cell profiling
• Read about the metric we use for quantifying phenotypic strength in A versatile information retrieval framework for evaluating profile strength and similarity

I have profiles made from Cell Painting data. How do I explore biology in them?

• Watch the videos The beginner’s guide to morphological profiling (Morphological profiling, part 1) and The beginner’s guide to morphological profiling (Morphological profiling, part 2)
• Read the blog post Interpreting Image Based Profiles
• Follow the protocol Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization.

How do I understand Cell Painting features?

• Start by watching Ask Erin Dear Beth Episode 25 - Interpreting Cell Painting Features: Classic Cell Profiler Features for a casual podcast explanation.
• Read What do CellPainting features mean in the Cell Painting wiki
• Read How measurements are named in the CellProfiler manual
• For more specific details on any specific feature/measurement, read the Definition of all measurements in the CellProfiler manual.

How do I find published Cell Painting data to explore?

• The Cell Painting Gallery hosts a LOT of published Cell Painting data and is free to access. Read Cell Painting Gallery Documentation.
• JUMP Hub has a set of introductory and advanced data exploration tools for JUMP, a single large Cell Painting dataset.

I need more help. What should I do?

• Ask questions in the https://forum.image.sc/ or search there through the rich archive of other people’s questions.
• Get a hold of us! See Collaborating with the Imaging Platform for the ways that we can help you.