angelolab/ark-analysis

OME-TIFF to single channel workflow fails if metadata not contained

alex-l-kong opened this issue · 0 comments

Describe the bug

Some OME-TIFFs don't have metadata in a format that can be accessed by tifffile. In this case, the extractor would fail, since this is used to extract the raw channel names.

Expected behavior

If metadata cannot be extracted by tifffile, then the extractor should still work. However, the user will need to provide an explicit channel list.

Alternatively, see if there is another OME-TIFF reader that can parse these channel names.

To Reproduce

Luke Jones from the University of Birmingham had some example OME-TIFFs that threw an error that the metadata was None.