Im using CP for sometime now and really felt very thankful to all of you for such a great software.
I have some basic queries to be clarified:
*]How exactly, Integrated intensity is calculated?
Is it that once primary & secondary objects are identified, then we simply take the pixels falling into each object and then adding the intensity of each of these pixels together to get the integrated intensity. For example, nucleus.
*]I’m also wondering, how the area and perimeter of cells are calculated. Are any geometrical shapes considered for area calculation, especially irregular shapes like cytoplasm?
*]I guess, Mean intensity is simply = integrated intensity/area??
*]How can we convert area into number of pixels and volume, if needed?
*]Whats the size of the pixel considered during analysis? Is is fixed or varies from each set of images?
*] Since, nucleus is having nucleolus (mostly multiple), is there anyway by which we can remove the area occupied by nucleolus so that we can get the actual Mean intensity by using refined area. This is because, many a times nucleolus cant be stained with dyes like DAPI but while calculating we consider whole area against only stained parts by dye as integrated intensity?
Thanks a lot for making me understanding all these issues.