Improve ImageJ's handling of large (>4GB) TIFF files
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- Dominant language
- Java
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Description
It should be possible to quickly load, browse and save very large TIFF files in a coherent way. There are several pieces to this:
- [ ] Ensure SCIFIO transparently writes to BigTIFF when exporting using File > Export > Image...
- [ ] Make SCIFIO able to import ImageJ1's "raw pseudo TIFF" format
- [ ] Make SCIFIO's "virtual stack" (cell image) performance as good as possible
- [ ] Make SCIFIO recognize signs (e.g., an ImageJ1-style ImageDescription in the first IFD) when a TIFF is written monotonically, so it can be parsed more quickly (i.e., without explicitly reading all the IFDs)
- [ ] Make SCIFIO add such signs (probably some new metadata as a directory entry in the first IFD) when writing TIFFs
Also critical is to improve performance of Bio-Formats `setId` calls of various high-impact proprietary file formats such as ND2, although that work is outside the scope of this issue.
See also these mailing list threads:
- [Problems with Saving Tiff greater than 4 GB & bigTiff exporter](http://imagej.1557.x6.nabble.com/Problems-with-Saving-Tiff-greater-than-4-GB-bigTiff-exporter-tp5010074.html)
- [Processing huge files](http://imagej.1557.x6.nabble.com/Processing-huge-files-tp5012001.html)
- [bfconverter nd2 to tif](http://imagej.1557.x6.nabble.com/bfconverter-nd2-to-tif-tp5012133.html)
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Review the SCIFIO TIFF import/export and virtual-stack work described in the checklist, starting with File > Export > Image... and the raw pseudo TIFF and monotonic-TIFF cases. Break the issue into independently testable parts and identify focused performance checks for large files; completion requires addressing the checklist items, while Bio-Formats setId performance is explicitly out of scope.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- backend, performance
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100