Cell counting and Raw Intensity

Hi everyone, we are trying to process drosophila images, and we could use some help to get the information we need.
We are trying to count the number of cells and the intensity of each cell along its boundaries.

Input Image (662.6 KB)

The output we are expecting is something like this + Intensity along the sides of each cell (Raw Intensity)
Expected output (1.9 MB)

This is the first time we are trying to do such an analysis, so we are unaware of the tools used for this. We tried cell counter in ImageJ, but the results were not optimal. We are happy to use any new software or analysis tool for this, so if anybody can guide us through or provide a solution, we will be very thankful.
If any more information if required from our end, we will be more than happy to provide it.


You could use a number of tools to do this, but one that would work is CellProfiler- briefly, you’d want to invert the image (which you can do using the ImageMath module), use IdentifyPrimaryObjects on the inverted image to identify your cells (since it expects the objects of interest to be bright on a dark background), then MeasureObjectIntensity on the ORIGINAL image with your cell objects; there are a few different metrics to do with edge intensity (mean, integrated, etc) that would be appropriate depending on exactly what you wanted. Your display could be made with the DisplayDataOnImage and SaveImages modules.

Our YouTube channel and example pipelines are good resources to get started in this. Best of luck!


Thanks for the solution. It works like a charm!!

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