Yes, I have been very frustrated by this. We tried to make using the SciJava I/O mechanism (and therefore SCIFIO) the default for ImageJ2 and Fiji several years ago. But there were many complaints from users about SCIFIO being too slow with TIFF files, and failing to open some files correctly compared to ImageJ1. These tradeoffs are briefly described on this page:
The correct way forward is to fix the SciJava/ImageJ2-based mechanism to work as well or better than ImageJ1 in all cases. There are myriad advantages, such as:
- Extensibility compared to the very rigid
- True N-dimensionality and leveraging the ImgLib2 library.
- Full support for cell-based images (what ImageJ1 calls “virtual stacks”, but more powerful).
Unfortunately, in the past several years, no one in the community has had sufficient abundance of time and interest to address these performance and correctness concerns—SCIFIO has been “idling” so to speak as we’ve worked on more urgent priorities with limited available effort.
Fortunately, that may finally change now, since my group has recently secured funding for continuing core work on ImageJ2 and friends for at least 5 more years. But in the meantime: you’ll have to either live with the tradeoffs of the “Use SCIFIO when opening files” toggle, or find resources in your group to attack the problem and make things better.