Can you use metadata in HDT file to assign channel identity?

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:

[program]_[well]w1.tif
[program]
[well]w2.tif
[program]
[well]w3.tif
[program]
[well]_w4.tif

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.

Thanks!
-Adam


Hi Adam,

I posed the question of the wavelength assignment to our resident microscopy expert here and he said the following:

Is this something you can check and/or is upgrading an option?

As it is, the short answer is: no, LoadData cannot use these files to load the images.
-Mark

Hi Mark,

Thanks for your reply - I do think we can update the MetaXpress version free of charge. We’re running v3.1.0.89 (Oct 18, 2010); do you happen to know if versions newer than that have fixed this problem? Just FYI, I called Molecular Devices, and in their database of requested changes, they have this bug listed as “not yet fixed”, but the tech support guy told me that doesn’t necessarily mean anything - apparently fixes aren’t always recorded.

best,
-Adam

Unfortunately, I don’t know this for certain. However, to my knowledge, I haven’t encountered this issue from recent data coming off our scopes.
-Mark