I would like to know the analysis method of 3D cell painting

I’m trying to perform 3D cell painting, can you tell me the general methods and settings using Cell Profiler?
The machine uses Yokogawa’s Cv8000, but I don’t think it has a proven track record, so other equipment can be used as an example.
I am waiting for a reply from a kind person.

Hi @daisukekubota,

If you are a beginner to CellProfiler, please go through the tutorials which would help you to start with from here,

The sample 3D pipeline is available here with the quick start guide.


This tutorial also includes a 3D component that works through the 3D example on GitHub: I2K 2020 tutorial: Introduction to Image Analysis and Machine Learning With CellProfiler and Cell... - YouTube

Corresponding tutorial materials: tutorials/3d_monolayer at master · CellProfiler/tutorials · GitHub

Good luck!