(SOLVED) Calculate proportion of positive cells

Let me first say how great and powerfull your software is (CP and CPA)! I work on a high throughput project, involving thousands of images for each experiment, and this is really going to be helpfull.
However, I must say that I have not been able to do something I thought would be easy to do with CellProfiler and CellProfiler Analyst:

Let say I have for each photographed field two images: one is a DAPI staining, used to count the cells (works great), and the other is a GFP staining, used to detect “positive cells”. All the cells are not GFP positive, and all the positive cells are not equally positive (some have high integrated GFP signals, some lower integrated GFP signals).
My data is way too large for a spreadsheet, and is thus sent to a SQLite database, and I know zilch on SQL language and or table operation.

My question is:
How can I determine the % of GFP positive cells?
Sound simple, isn’t it?


Have you tried using the “Cell/particle counting, and scoring the percentage of stained objects” pipeline from our examples page? If not, it seems like this would do what you want…


Hi Mark,

Thanks for your “to the point” answer, which indeed provides me with a solid starting point. One problem though, that has already been treated in this forum: the output of a module (TRUE) that my SQLite db does not want to digest. Otherwise, great!

Philippe, another one who did not go thoroughly through the F… manual before posting.

Hi Phillipe,

I believe we’re dealt with this issue in our code-base, but have not released it as yet. However, it is included as a developer build of CellProfiler which is available from here with the caveats mentioned on that page. If you’re daring, give it a try (take note of the fact that pipelines made with the trunk build are not backwards compatible).