Opening OME-TIFF with drag & drop in ImageJ/Fiji

I’m starting to use tiled and/or compressed OME-TIFF images more and more, and I find it isn’t possible to open these in ImageJ or Fiji directly by drag & drop.

There is invariably one of two error messages:

  • ImageJ cannot open TIFF files compressed in this fashion
  • ImageJ cannot open tiled TIFFs. Try using the Bio-Formats plugin

Opening through the Bio-Formats plugin works fine, but is there a trick to get drag & drop to work?

Or does it need a change to ImageJ1 to try Bio-Formats when the built-in TiFF reader fails?

I think the relevant code is here where HandleExtraFileTypes is not given a chance if the image is recognized as TIFF.

I know from others that some OME-TIFF images work with drag & drop, but my guess is that these must be neither tiled nor compressed, so that ImageJ’s TIFF reader handles them. But if so, it still seems preferable to use Bio-Formats for metadata-parsing reasons.

Thanks!

1 Like

Can confirm issue, drag and drop works with non-tiled OME.TIFF images only.

Hi I just reproduced this, annoying isn’t it. I’ve alerted the appropriate people :wink: This is a new error. I wasn’t having a problem with 2 weeks ago. Not sure what has changed. A

1 Like

Thanks @A.P_Wheeler and @Research_Associate!

I find that if I go to Edit → Options → ImageJ2… and turn on SCIFIO then my OME-TIFFs open very nicely with drag & drop. The trouble is that ImageJ TIFFs open differently… most importantly, they don’t have the ‘origin’ property set, which is something I use within QuPath to relate small images extracted from whole scans back to where they came from.

It would be very helpful if either

  • ImageJ1 allows Bio-Formats to have a go at TIFFs it cannot understand (or, preferably, all OME-TIFFs - even untiled and uncompressed)
  • SCIFIO could read ImageJ TIFFs in a way that closely matches how they are read by ImageJ itself
4 Likes

Sorry for the long delay in reply. Of course, we want SCIFIO to handle ImageJ1 TIFFs correctly. The fact that it doesn’t is a bug. It would be helpful if someone would file an issue for it. And I believe @tpietzsch was also just today investigating a similar issue—so maybe there will be news there soon.

See also:

2 Likes

Upgrade to the current version of ImageJ (1.53a) using the Help>Update ImageJ command and you will be able to open compressed OME TIFF files using drag and drop.

3 Likes