I first wanted to say thank you for the quick and helpful responses I receive on this forum- I am quite new at this program and I have a lot of quantification to do for my lab and the help has made this task less overwhelming.
My problem is as follows: I want to measure integrated density of an entire cell, but also obtain the mean intensity of a certain region of this cell. For wild type cells, the region that I need the mean intensity for is basically the entire cell, however it is very difficult to identify the mutant cells correctly since they have many structures the wild type does not, and I am not sure of the best way to use the identify objects modules to distinguish between these messy regions and find only the region I want to measure.
My idea was to identify primary objects as full cells, and use the manual identification module to circle the region of interest in the cell, in order to measure the mean intensity of this region separately from the rest of the cell. However I do not know how objects are numbered or how this information is stored by CP; I usually just export measured values to a spread sheet and use the data without worrying which number belongs to which cell. But if I am to identify primary objects and then manually circle regions withing those objects, I need to make sure that each primary object corresponds to the region I circled using the manual identify module, and then measure intensity for both objects and export. Is there a way to identify primary objects and see the individual labeled numbers during manual identify? Any help or explanation to how I can do this project would be greatly appreciated!