Cell Profiler pipeline for Image area

I am having trouble making a pipeline to calculate the area of the image.

I am not too expert with the threshold and image processing. I have hard time understanding which value is indicating the area of the cell.

Hi Treza

Area occupied by object is the amount of pixels in the total objects (42000)
The total area is the amount of pixels in the full image (200000)

So you have 20% of your image is objects.


Thank your for your reply.

So the area occupied under threshold is the real are of the cell (white)?

Also then what is the MeasureObjectSizeShape area Indicating? Like the mean and median.

The module “MeasureObjectSizeShape” produces the window which shows shows the mean and median of all the individual cells found.

The module “MeasureImageAreaOccupied” produces the window which, as @lee.marshallsays, tells you the total area of all cells in the image.

Thank you for your answer.

The picture is actually of a single cell. I mean the total white area is one cell and because of the resolution it is portrayed as dot dots. So does this mean MeasureImageAreaOccupied should be the area of the cell (all the white portions)?

Thank you

Ah, I see. Yes, indeed!

Thank you so much for helping me determining the area,

I need to determine the intensity as well


Is this the correct pipeline to determine intensity?

also the program is selecting dots inside the area. how do I make sure it is focusing on the area I want it to focus on eliminating the side dots and the dots inside the black (original picture)?

You could indeed use that pipeline - you can export the intensity values for the individual “objects” (in your case, chunks of cells) and in the resulting spreadsheet, total up the column “Integrated Intensity” and that will give you the total intensity.

It’s a bit simpler to instead mask the image and use MeasureImageIntensity, but I am not looking at the modules/settings right now so I can’t provide specific advice on how to set that up.

Thank you so much for your help. Is it possible to post the pipeline here? I just want to make sure that it is measure extracellular intensity but not internal.



How do I make sure that the object selected it the only white area? This seems to select every dot.