Resampled Autofluorescence File is completely blank about clearmap2

[nicolasrenier]

I have to admit that certain tif formats can be a pain. We use ClearMap with the ome tiffs, but sometimes when we import tiff data coming from other sources it can be a problem. My recommendation is to convert the files to a less capricious format, such as the npy arrays, or I found nrrd works well for the most part. But depending on your sources, this might take a few tries to get the right format that can be opened with the tifffile library. ImageJ with BioFormat can really help in most cases to do these conversions.

[SaibotMagd]

I found the solution: "convert the tif-files to npy-files before resampling". Why? I don't know.

Quote from TubeMap Tutorial: "

Tile conversion

ClearMap makes use of accessing binary files in parallel. 
For optimal performance we recommend to convert the data to numpy files.

I think this is evidence that this isn't just "recommended". It actually changes the outcome.

[ZachPenn]

Thanks for posting your fix to this @SaibotMagd! I ran into the same issue with .tif stack files, and really didn't want to continue dealing with folders of thousands of ome.tif files -- the conversion to npy worked great for me.