Implement TIF import without Bioformats in GUI#756
Merged
Conversation
The multipage TIF export function has exported each channel to a separate file. Provide an option to export all channels to the same file and make this option default. This change allows the exported TIF to be imported back to NPY format.
Move into module level function.
Implement the TIF metadata reader using `tifffile` in place of Bioformats in the import pathway.
- Load TIF files through the dedicate TIF reader instead of using Bioformats in the import pathway - Implement fix for saving files in Numpy 2 - Allow running the import pathway when Javabridge cannot be loaded and remove warning
Add channel dimension if missing since the GUI expects the shape for all 5 image dimensions.
Use the array dimensions directly for this shape rather than the shape from the channel setup.
yoda-vid
added a commit
that referenced
this pull request
Oct 24, 2025
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes #752.
Implement the multipage TIF loader through
tifffilein the Import tab to allow import without the command-line. This approach also uses the existing import controls to import images split into separate images for each channel.Additionally, the CLI export to TIF now writes multichannel images by default rather than splitting into separate images for each channel now that these images can be re-imported through the CLI or GUI.