How to Open a Stitched Image from BigStitcher/BigDataViewer in ImageJ

Hello All,

I’ve been working with a large data set that I’ve been stitching with bigstitcher. Up to this point this has been more than sufficient to cover my needs for checking my data quality, but I need to do more with it,


  • I have a big data set (20x25x49) of 1024x1024pixel tiles with two channels each (All the useful data is in one channel)
  • It stitches just fine with bigstitcher and displays in bigdataviewer

My problem is that I need to do the finishing touches and display methods to this stitched stack. I know how to do all the things I need in ‘regular’ FIJI/ImagJ but am having trouble exporting the stitched stack as an image stack into that environment. Is there some method of doing this that I’m missing or can I do the following in BigDataViewer?
Things I need to do:

  • Brightness and Contrast adjustment (This is just in the settings of the viewer.)
  • Add scale bars
  • Display an orthogonal 3D view of the stack (Seems to be more of a slice through the current tile rather than a 3D image.)
  • Display an orthogonal blown out view of the tiles (VizBio)

@bogovicj @StephanPreibisch @hoerldavid @tpietzsch or anyone else? If you want access to my dataset let me know.

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Hi @Niklas_Gahm,

Welcome to the forum.

Have you used bigstitcher to do the “Fuse and export” and if so how did you export your stitched stack?

There is an option to display the stitched result in imageJ see here. Maybe that would suit your needs?

I’m not sure what you mean by your last point exactly:

But the first three things can be done with bigdataviewer (bdv).

  • S brings up bdv’s brightness contrast options.
  • Getting the scale bar depends on how you have things set up…
  • (Shift+ Z), (Shift+ X), and (Shift+ A) can give you various orthogonal slice views.

if you have questions about these please post back and we’ll help you get there.


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