Hi All,
I want to use CellProfiler and program it to identify an object as a cell from an image and count all the other object that have the same parameters/measures as the object I initially specified.
In the image I attached, say I want CellProfiler to identify this object (in yellow circle) and measure all objects that have similar size or shape in the rest of the image - how do I do that?
Hi Sherief,
you should use the function "Identify primary objects".
The function is quite complex but in essence does the following:
-Separates background (no cells) from foreground, by intensity threshold
-tries to separate touching cells in foreground by watershed methods
Start with finding a good intensity threshold. first manual, if this doesnt work try the automatic global ones. if they do not work, try the adaptive ones.
Next, try to find best parameters for objects separation. A bit of background reading, what a watershed does, will be helpful.
Best
Christoph
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