Unable to analyze an OME-TIF file after conversion with comstat2


I am having an issue with getting Comstat2 to recognize an image file even after conversion to OME-TIF format. My original file is a .LIF file that I can not open inside of imageJ with comstat, but it does open successfully with FIJI, and I can process the bio-format exporting into a .OME-TIF file. So I thought I could perform the conversion of the file in FIJI into OME.TIF and then process the OME.TIF in comstat2. When I port the directory of comstat2 to the folder containing the images, they appear in the list but the carrot disappears when clicked instead of opening channel options. I have an example OME-TIF that works correctly so I know it has to be the converted file that’s a problem. I read the comstat2 manual and identified the section in the troubleshooting:

“Nothing is analyzed even if the files are shown in the Images in Directories box
When adding a directory, which contains lif, lsm or ome.tif files you can see the file name in the Images in Directories dialog box, but nothing is analyzed when you run the program. If you click the triangle (Mac) or key symbol (Windows) next to the file name, the symbol disappears where you would expect the stack list for that file. This problem can happen if the file contents is not acceptable by Comstat2: For instance, newer versions of the Leica LIF format do not comply with Comstat2 while older do. Likewise some ome.tif files cannot load correctly, if they are generated with a program that does not 100% adhere to the OME-TIFF standard (an example is Imaris prior to version 8.0.3). Another situation resulting in the same problem is if the file contains “stacks” without a z-dimension, such as xy-snapshots (single planes) or 3D-renderings (pertains primarily to Leica LIF files).”

This is obviously what’s happening in the situation but I have no way to resolve it. Any assistance would be very helpful.

Thanks so much

Hi Jeff, sorry similar to Comstat install issues - #2 by etadobson I’ve no experience with comstat2 but mentioning @comstat seemed to help there.