I’m trying to run Cell Analyst but have thus far been unsucessful. I can run the Cell Analyst example file just fine but when I try Cell Analyst with my CellProfiler generated database, it doesn’t work. I’m attaching my setup script, preferences (without username or password), and data files generated by CellPofiler as well as the java output file. It seems like I can connect to the database, but nothing happens when I open the preference file. One problem I can see myself having is with the CPcreatesql and the CPcreateCPAProperties subfunctions. In CellPofiler, I take nuclei and then find cells. Then I clear the border of cells found and also of the nuclei those cells were associated with (this takes care of the case in which the nuclei does not touch the border but the cell does). I then consequently do measurements on the border cleared cells (labeled BCell and BNuc - I had to shorten the names because of the matlab character limitation thing). However, this leaves a nucleus data set and a borderclearednucleus data set. The export function doesn’t seem to match these datasets up - I think it assumes that the first data point of each object type is the first data point of every other object type - this does not seem to take advantage of the parent protperties of each obejct (even though they’re calculated). I guess I was wondering if you all also precieve this problem to be the root cause of Cell Analyst failing as well, and if you guys had any suggestions to solve this. I was thinking of going through and editing the aforementioned CPsubfunctions, but I wasn’t sure if I could get it to behave intelligently enough (maybe just write something in to get it to ignore certain object types so I wouldn’t need to export them?). I guess the other thing I could do would be to merge the identifyprimaryobject and identifysecondaryobject modules in to one large module that would be able to do the border clearing without the need to then write the non-border cleared objects to the handles structure. Anyways, if you’d like to see the actuale handles file, please let me know (as it’s just a tad over the upload limit) and I can email it to you. Well, thanks so much for the work thus far. Any help that can be provided would be very much appreciated.
P.S. - The more I think about the problem, the more I think it probably originates in my creative use of Cell Profiler, so I was wondering if it would be better for me to also cross-list this problem in the Cell Profiler help section?
SQL.zip (1.08 MB)