Puncta per Cell

Hi everyone,

I am trying to use CellProfiler to indentify/count punta in A549 cells. I’d like to (if possible, I’m new to CellProfiler) count the number of cells in an image, and the number of puncta in each cell. is it possible to assign the total number of puncta to a specific cell?Ideally I’d like to get a Puncate per cell measurement. Cells size range between 15 and 60 pixels in diameter for a 20x magnification. Punctae is around 2-9 pixels in diameter. here is some sample images I’m working with, any help is greatly appreciated! Thank you
20210107_FITC_10.tif (8.0 MB) 20210107_FITC_14.tif (8.0 MB) 20210107_FITC_20.tif (8.0 MB) 20210107_FITC_30.tif (8.0 MB) 20210107_FITC_01.tif (8.0 MB)

Hi @namaya13,

Welcome to the forum.

Have you looked at the example pipelines on the CellProfiler website? The one called Speckle Counting sounds like what you need.

Hi Laura,

Yes, I did. However; It did not work very well with the images I have. Maybe I need to spend a little more time changing the parameters. I would like to know if there is a way for me plot a distribution representing the number of punctae per cell, not a mean but rather a specific number punctae and which cell it came from. do you have any advise?

It might be useful for your progress if you upload the pipeline that you have so far and describing which parameters or modules you’re having issues with.

CellProfiler exports a number of results CSVs, the “Image” holds image level statistics (how many cells and punta in each image). If you have used RelateObjects then you will be able to get number of cell per punctae but it will be in the object CSVs. The “Cell” csv will have puncta listed per cell and the “Puncta” csv will have a column listing which cell is it’s “Parent”.

As I say, if you upload your pipeline it might be easier as the answers can be more specific to your situation.

Hi Laura,

Thank you for your help. Here is my pipeline. I’d possible like to export the data so that I can plot it using MATLAB or other software but basically I’d love to be able to plot a distribution of individual cells and their respective punctae. Thank youCellCounter.cpproj (441.6 KB)

So the issue was that you were selecting which measurements you wanted to but were missing the one you want (see below).


Now that I have ticked that, I ran the pipeline with no other changes and the “CellCountCells” spreadsheet looks like this


So you should be able to plot what you are after.

Hi Laura,

Thank you so much for your help!

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