Reading z-calibration in ome.tif with ImageJ

Hi @dgault @joshmoore @ctrueden @imagejan,

I am sorry when this has been asked already in some other thread.

Opening attached file gives a wrong pixelDepth ([Fiji >Image > Properties]) of 1 micrometer when opening via drag and drop onto Fiji.

However when opening it with the BioFormats plugin if gives the correct pixelDepth of 10 micrometer.

image–C00–T00000.ome.tif (2.2 MB)

Am I doing something wrong?

Best, Tischi

Opening any .tif file (no matter whether it also contains .ome) by drag and drop will always open the image with ImageJ1’s own TIFF reader (if I’m not mistaken).

In order to ensure that the OME metadata are read correctly, you’ll have to explicitly go via Bio-Formats (File › Import › Bio-Formats) or SCIFIO (File › Import › Image… ).

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Thanks for the clarification. This is obviously not great for the users. In fact, this may even lead to wrong scientific results if people do not spot the wrong z-calibration. In my experience that is a likely thing to happen. But I guess there are technical reasons for this that are hard to fix.

I was under the impression drag and drop behaviour changed in ImageJ 1.52u, following the post below. Can someone please confirm?

Although without calling Update ImageJ… it may not have found its way into the latest Fiji build yet.

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I updated to 1.53a and am getting this when opening above file:

So, I cannot confirm, seems to still not use the BioFormats Tiff tags for the calibration.

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 HandleExtraFileTypes approach.
  • 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.


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