Problematic modification in opening ome.tiff files

[houllier1]

Hello,
For the past 2-3 weeks, I've been having trouble opening ome.tiff files. Previously, even if there was a metadata.companion file and several files of the same series named incrementally, when I dragged and dropped a file it opened directly and quickly by indicating the file name in the window. This still works with FIJI 2.9.0 and imageJ 1.53t.
However, with version 2.16.0 of Fiji and 1.54g of ImageJ, a window opens with the whole series and this slows down file opening considerably. The name indicated in the window is changed to metadata.companion - acquisition date. If I delete the metadata.companion file from the folder, the file opens as if there were only one channel (instead of 2) and no z.
Have there been any recent changes in support for ome.tiff files? Is there a way to change the file opening parameters without using an older version of FIJI?
have a nice day

[ctrueden]

@houllier1 I notice that ImageJ 1.54k fixes a "bug with IJ.openImage(path,n) opening .ome.tif files" according to the release notes. So maybe doing a Help → Update ImageJ... and switching to 1.54k will address the issue for you? Let us know your findings. If not, it might be a change in the Bio-Formats plugin for ImageJ, which is what handles OME-TIFF file imports.

[houllier1]

@ctrueden
Thanks for your answer
I tried with the FIJI 2.16.0_IJ 1.54m, k, i, h versions and FIJI 2.14.0_IJ 1.54i version, and i had the same problem.
I just downloaded and used IJ v1.54g alone not in FIJI bundle, then it works.
With the FIJI 2.16.0 downgraded with IJ 1.54f version, it works. In this case, the file open directly and not with the Bio-Formats import window.
Thus, I think that the problem come from the Bio-Formats plugin in the FIJI distribution since the IJ 1.54g update.

I found a solution with the 1.54g versions and later. I just renamed my files without ".ome" and it works now.

[ctrueden]

@houllier1 Thanks for following up. Probably the best way forward then would be to report the bug to the Bio-Formats team. One easy way to do that is to post on the Image.sc Forum in the "Usage & Issues" category with tags bio-formats and fiji and mention @ome in your request. (It would be nice if we could transfer this issue report to the Bio-Formats issue tracker, but GitHub only allows issue transfers between repositories of the same organization.)

Edit: One nice thing about the forum (rather than GH issues) for this particular problem is that I'm not 100% certain the issue is with Bio-Formats... it might rather be something that needs to be fixed on the Fiji or ImageJ side. Historically, Bio-Formats couldn't control the drag-and-drop behavior of ImageJ itself; the core ImageJ TIFF reader (not Bio-Format's OME-TIFF reader) would be used always, which it sounds like you were relying upon. The upside is it's faster; the downside is you don't get proper multidimensional interpretation for 4D+ data.