Problem when opening metamorph files in FIJI

Hi all,

I’ve found a weird behavior when I open metamorph nd files in FIJI. Specifically, if the name has an underscore followed by a number in it and there is more than one dataset with the same basename the window’s name in FIJI when I open the file is incorrect.

For example, for three metamorph datasets named run_, run_1 and run_2 consisting of a single plane with 2 channels, I have the following files:

run__w2Fast - TxRed.TIF
run_1_w2Fast - TxRed.TIF
run_2_w2Fast - TxRed.TIF

Note that the verbose part (example: w1BF-Phase-acq) is a descriptor of the setting used to acquire each channel, which in my case gets added automatically to the TIF file names.

When I open run_1 by dragging the nd file into FIJI, the window name is run_1_w1BF-Phase-acq.TIF

When I open run_2 or run_ by dragging the nd file into FIJI, the window name is also run_1_w1BF-Phase-acq.TIF, though the image shown is the correct one.

If, instead of an underscore, the files have a space, a dash or no space at all between the basename and the number, then window names have the proper number.

Metamorph version is, which I believe is the latest. FIJI (including BioFormats) is udpated as of today 2019.Aug.12, and is running ImageJ 1.52p.

I can provide a link to the minimal example described above, if that would be useful.



Have you tried importing your images using Bio-Formats (File > Import > Bio-Formats)? The drag/drop method to open files does not use Bio-Formats. See if “Use SCIFIO” is checked in the “Edit - Options - ImageJ2” (read more on SCIFIO [here]). If unchecked, ImageJ is using its own internal libraries… so might have issues.

So try via SCIFIO and/or Bio-Formats. You can also share your image files for us to test as well.

SCIFIO was unchecked; checking “Use SCIFIO” on made the drag-and-drop work properly; thanks for the suggestion!

Using File->Import->Bio-Formats gave the same result as dragging and dropping on my system (before checking SCIFIO on): run_2 image showed up with a run_1 name. In short, SCIFIO fixes the problem, though it is weird that Bio-Formats can’t handle it.

Sample dataset is here, in case anyone wants to play with it (bunch of files in a zipped archive):


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