How to deal with data produced with CellProfiler?


Hello everyone,

I am quite new to CellProfiler but I think I created quite good pipeline for my images from genom-wide RNAi screen.

But the problem is that I am not familiar with programming and this kind of things… so now here comes the question: how to analyse the data in the simplest way? I mean, I saw that I can export them to excel as csv file…but what next? What can I do later with such a file?
I thought at the beginning that the easiest to use will be CellProfiler Analyst but for that I need to export my data to some database? Or I can use csv files in CellProfiller Analyst? If yes, then how can I generate properties file for CPA (when you use database option it is generated itself, right?) But what when I do not want to use database but csv files, how can I get properties file?



Hi Anna,

First of all, congratulations on your pipeline!

“What next” is an excellent question, and really depends on your particular situation. Do you want to extract something super simple like cell count, or something really complicated like a subtle change in cell shape? How comfortable are you (if at all) with tools like Python, MATLab, R, or do you have a colleague or friend who is comfortable with them who can help you out? All of these factor into what your personal best next step should be.

If you want to be able to use CPA, you’re right you’ll need some kind of database- if you don’t want to have to deal with tangling with your university/company/etc database infrastructure, you can use the ExportToDatabase module set to the SQLite option- an SQLite database is essentially just a “wrapper” around a bunch of spreadsheets, so you can run it locally on your hard drive. You can indeed also configure ExportToDatabase to make the properties file you’ll need for CPA. If you also want the CSVs, you can have BOTH ExportToDatabase and ExportToSpreadsheet; many free database reader programs will also allow you to open the SQLite database and export each table as its own CSV.


Hi @Anna2303, I just recently started using CellProfilerAnalyst to get a grip on screening data that we got from 96/384well plates.
I must say I really like it a lot and I can definitely recommend it to give it a try, especially if you have data that was acquired in well plates.

As @bcimini wrote, [quote=“bcimini, post:2, topic:4961”]
you can use the ExportToDatabase module set to the SQLite option

Additionally, in the same module, check “create CellProfilerAnalyst properties file”.

Your settings could look similar to screenshot below, with the exception that you should probably set “Access CPA images via URL” to “No”

After running your CP pipeline, just start CellProfilerAnalyst, select the *.properties file and start exploring.

Depending on your assays readout, you might also check out Genepattern.

CellProfiler has an output option for this as well, you find it in the “ExportToSpreadsheet” module where you can “create a GenePattern GCT file”.

I am not familiar with GenePattern, but quoting the website:

GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a Web interface with no programming experience required.

Hope this helps!


Thank you guys a lot! I will try your suggestions :slight_smile:
Best Anna