CellProfiler cell and subcellular compartments analysis

Hey everyone, I’m very new to CellProfiler and imageJ. However I just started a new project that requires me to use either for my confocal microscope image analysis. After going through the litreature, I have concluded that it is better to use for high throughput image analysis. What I intend to analyse is nuclear morphology of human cells. But i woul like the software to recognize cells, and recognize nuclei inside the cell, count them, and report how many nuclei are in every cell. Also I would like some additional info about these nuclei and cells, such as their size, the ratio of their sizes between each other, the circularity of the nuclei, and the surface area of both cells and the nuclei inside it.

I would appreciate if someone would take a bit of time to help out!

Hi @AliNassar,

It sounds like you should be able to do this in CellProfiler. You might want to start with some of the segmentation tutorials to learn the software, but for the actual analysis I'd focus on using IdentifyPrimaryObjects and RelateObjects modules to identify Cells and Nuclei then associate them with each other. You could then exploit the MeasureObjectSizeShape module to gather the additional statistics you mention.

Hope that helps

Hi @AliNassar,

You also try & start working with the basic example pipelines (Human Cells for Cells & Nuclei segmentation). Further you could also start changing the parameters & modules according to your requirement.

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