I just begun using CellProfiler for a project (I usually use more custom build algorithm in Java or Matlab), and while I appreciate how nice a tool it is, I must admit I am having trouble understanding how CP deal with multidimensional data. As I understand it, CP is doing a loop on 2D images and those 2D images can be grouped in various ways if need be (time frame of a movie, or z-stack plane, say). But I could not find where/how CP keeps track of that, i.e. concatenating objects from all image in a group for further analysis in a module or analyzing all images of a group at once, for example.
I had a look into the tracking example provided in the web site, and as I understand the memory is kept within the tracking module itself, not in the workspace, i.e the tracking module is the one keeping track (hum) of what he saw in the previous 2D images, the workspace would only know about the current 2D image. I am getting it right? For what I had in mind I do have to have access to all objects in a group (i.e. objects from all time points), the way to do that would be inside my own module?
More generally, how is CP dealing with data up to 5D, with x-y-z-time-channels (that I usually have in other projects)? Unless I missed something, that would be tricky to do with the one level of grouping currently available. I would think having nested loop and/or dealing with more than 2D would become needed at some point, but it might go against the simplicity and usability principle of CP?..
Many thanks for the answer (and sorry if I just missed it in the doc)…