Hi all, I’m using the software Metaxpress and a high content microscope to take lots of images, and exporting them so I can analyze them with CellProfiler. For each well, I’m having it take one image, four channels. So Metaxpress naturally names them as follows:
Each of these corresponds to a channel - DAPI, FITC, Cy3, or Cy5. The problem is that, despite me running the same program over and over, Metaxpress randomly assigns which W# goes with which channel for each new plate. I can visually inspect the images to figure it out, but I’m planning to do a lot of plates, and that’s just not feasible over the long term. The information is stored in an HDT file that gets exported along with the images (the “WaveName” rows - see attachment), but I can’t figure out if there’s a way in CellProfiler 2.0 to use that kind of file. The LoadData module is able to read it as if it were a CSV file (when I click the “preview” button), but it can’t seem to do anything else with it. Any suggestions? Even just letting me know if it’s impossible would be a big help. I’ve attached a screenshot of the HTD file (as text), in case it helps.