Always open TIFF with Virtual Stack


I have been using SCIFIO to open my images lately and I find that sometimes a TIFF will open as a virtual stack and sometimes it does not. ImageJ will usually stick to one of the two methods until something “fixes” it. I have not been able to recognize any patterns here, but perhaps a setting is getting reset and ImageJ isn’t using SCIFIO temporarily?

I would really like ImageJ to always use a virtual stack because its faster and prevents out of memory situations. Is there any way to make ImageJ always default to opening the TIFF as a virtual stack?


Just to clarify, which flavor of ImageJ are you using? I am assuming it is either ImageJ2 or Fiji. In that case, have you tried checking the setting mentioned here? If you are using ImageJ1, you can just drag’n’drop it on the “More Tools” menu to open it as a virtual stack.

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I should have been more clear. I am using FIJI and it is fully updated and I am using Linux. After looking at the issue more carefully I think that the problem lies in the single instance listener. When I click on a TIFF in my file browser it opens FIJI and opens as a virtual stack. If I then drag and drop another TIFF onto the main FIJI window it again opens as a virtual stack, but when I click on another TIFF in my browser it actually opens twice, once as a regular stack (not virtual) in the same FIJI instance and once more as a regular stack in a new FIJI instance. Strangely the second FIJI instance does not show the main window. I have verified the second stack opens in a separate instance by closing the original FIJI main window and it only closes one of the images. Also I notices the window icon of the first image is FIJI’s, but the window icon of the second image is the standard Java icon.

That is definitely an interesting situation. Have you tried drag and drop the third image?

I just tested with a third image. Dragging and Dropping opens it as a virtual stack. Opening it from the browser repeats the same behavior (two images open, one in same FIJI instance, one in a totally new Java instance).

The previously described behavior is for TIFF stacks of multiple images. If the TIFF file contains just one image when opening multiple files from the browser it opens the first image as a virtual image (shows (V) in titlebar), and the second and onwards as regular images, but unlike in the TIFF stack case it doesn’t open the image twice in a separate java instance.

I have also checked that in the separate java instance the typical FIJI keyboard shortcuts do not work (like Ctrl+Shift+C for brightness and contrast).

Maybe @Wayne or @anon96376101 have an idea of what is going on.

Today I encountered a colleague who’s FIJI opened every tif as a virtual image (V) and only by using bioformats importer could you open a tif normally.
The problem persisted even after using a new download of FIJI & resetting FIJI preferences. The suggested solution of unticking ‘Use SCIFIO when opening files (BETA!)’ solved the problem. They must have inadvertently activated it somehow, although i am yet to understand how it persisted through a new install and reset. Thanks :grinning:

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@BC3D I am also having the same issue. Every time I import a tiff stack through File > Import > Image Sequence… FIJI imports a virtual stack (V) first before prompting the Sequences Options window. I checked to make sure that “Use SCIFIO when opening files (BETA!)” was not checked under Edit > Options > ImageJ2… I am not sure what to do. I have tried new install and reset but the problem persists. It was working fine a few days ago. It makes my macros unusable.

Hi @Steven_Wellman ,

Sorry I haven’t come across this and cannot replicate it on my system so we will have to wait for some else with more know how than us to answer this problem.

I assume this is only happening on a single computer/account? You could maybe try another user account to see if its an issue with the FIJI preference file? If so maybe a reset or deletion of preferences might be a solution.