Vanilla TIFF does not support labeling dimensional axes. Two initial options which occur to me:
- Save as an ImageJ (1.x) flavored TIFF, with dimensional metadata in the TIFF comment.
- Save as OME-TIFF, with OME-XML in the TIFF comment.
Here is the ImageJ format:
In ImageJ tradition, most of those fields are not required and have sensible defaults.
OME-TIFF is more complex but also more metadata-rich; see the OME-TIFF specification for details.
For either of these options, you may be able to surgically alter your original TIFF, rather than rewriting it completely. If your TIFFs are huge, this may be a time-saver. Happy to elaborate further if needed.
One other comment: Bio-Formats does have a certainty flag for each dimensional axis, indicating whether it is sure that its guess for that axis is correct. In the case of TIFF, the answer for that T dimension is definitely NO. So another option here would be to update the Stitching plugin to be more cautious about dimensions which are classified as uncertain.