Big Data Viewer / Big Stitcher causes havoc with gnome display manager (and other issues)

Hi all (@tpietzsch, @hoerldavid, @StephanPreibisch, @Christian_Tischer

I am struggling using Big Data Viewer and Big Stitcher for what it is intended, any help is appreciated. Currently, there are two issues I’m facing.

Brightness & Contrast Dialog in BDV kills Gnome Display Manager

First of all this is most likely a bug in Gnome, but I can reliably provoke it using Big Data Viewer and I think I can guess what is going wrong there. When I open a Big Stitcher Project file with 1256 tiles, and open the “Brightness and Contrast” Dialog in Big Stitcher this is what happens (on a pretty much out-of-the box Ubuntu 18.04) install.

The server is still running and when I logged in via ssh to look at the log file I saw that gdm3 crashed.
Granted, no user-space program should be able to cause this so I might have to raise that with gnome as well.
However, my (wild) guess is that is caused by Big Data Viewer requesting a window with very large dimensions and somehow this is not handled properly. Just to remind you what the “Brightness and Contrast” dialog looks like, this is the dialog for a project with a mere 144 tiles:

It is already challenging to interact with this as the dialog also has checkboxes for the individual datasets. My hypothesis is that for the larger dataset (roughly 8 times as many tiles) the requested window size for this dialog is causing the observed problems. BTW, on my windows laptop selecting this dialog kills the Fiji process.

Would it be possible to change this dialog to have a grid layout rather than a horizontal layout? Or alternatively to request a fixed size and have a horizontal slider?

separate issue: Big Stitcher stuck at “Preview Mode”

For the above project I decided simply not to adjust brightness/contrast for viewing and stitch anyway. So the pairwise shift calculation seems to happen fairly quickly, but I am stuck at the “Preview Mode” dialog. First the modal window with the title “Preview Mode” shows up and remains blank for a long time (40 minutes or so). Then the dialog shows the text "Pairwise shift calculation done. Switch to preview mode? Yes | No ". This is where the process is stuck. The preview mode doesn’t pop up and nothing happens. There is still some CPU usage from the ImageJ process (a single core seems to be used) but no indication in the log window as to what or whether any processing is happening. (nothing happens when pressing “Yes”).
I will leave this running overnight to see whether the dialog will pop up at some point.

I will add a dropbox link to the project once it has finished uploading.


Here is a link to the dataset in question - 1.2 GB large

I think it is a general issue that, currently, the BDV UI does not really scale for very many image sources.
@tibuch: Would your new UI solve that issue?

Yes, and we’re in the process of merging it.
However this is then available in bigdataviewer-vistools, not in bigdataviewer-core.
Probably we should put it in core as an alternative. Or provide a way to “patch” an existing BDV window with new dialogs.

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I think it would be good if also “normal users” that start Bdv from the Fiji UI could benefit from the improved UI.

Yes, I think so too, but one step at a time.


Thanks for the replies so far.

As a workaround, is there a macro command for setting the min/max intensity value, such that I can avoid opening the dialog?