Issue using Big Warp on tiff file

Hello!

I would like to use Big Warp with an SVG moving image onto a Tiff target image. Big Warp is working well for my SVG warping onto jpg and png files. However it is not working when I use my data file - a tiff image with three channels. It also doesn’t work on a single channel of the same tiff image. The target window is blank grey and I get this error message…

Opening <SpimData> dataset that is not suited for interactive browsing.
Consider resaving as HDF5 for better performance.
Exception in thread "PainterThread" java.lang.ArrayIndexOutOfBoundsException: 1
 at bdv.AbstractSpimSource.getSourceTransform(AbstractSpimSource.java:255)
 at bdv.tools.transformation.TransformedSource.getSourceTransform(TransformedSource.java:206)
 at bdv.img.RenamableSource.getSourceTransform(RenamableSource.java:53)
 at bdv.viewer.render.MultiResolutionRenderer.getTransformedSource(MultiResolutionRenderer.java:780)
 at bdv.viewer.render.MultiResolutionRenderer.createSingleSourceProjector(MultiResolutionRenderer.java:714)
 at bdv.viewer.render.MultiResolutionRenderer.createProjector(MultiResolutionRenderer.java:647)
 at bdv.viewer.render.MultiResolutionRenderer.paint(MultiResolutionRenderer.java:496)
 at bdv.viewer.ViewerPanel.paint(ViewerPanel.java:485)
 at bdv.viewer.BigWarpViewerPanel.paint(BigWarpViewerPanel.java:229)
 at net.imglib2.ui.PainterThread.run(PainterThread.java:86)

Any advice?

Thanks in advance,

Maria

1 Like

Hi @MariaZ

Thanks for reaching out here.

Have you updated fiji recently? And if not, could you try and see if that helps?

I’ll have a closer look tomorrow if that doesn’t solve this problem

John

1 Like

Hi @MariaZ,

I havn’t been able to reproduce this issue yet. :-/

How many channels/frames/slices does it have?
Also, I wonder what the look-up-table situation is for your image.

Could you copy the code below in the script editor, run it with your tiff image active, and report the results back?

Thanks again,
John

#@ ImagePlus imp

println( "nc: " + imp.getNChannels())
println( "nt: " + imp.getNFrames())
println( "nz: " + imp.getNSlices())
println( "nlut: " + imp.getLuts().length )

Hello! @bogovicj

Here is what I got with your script -

nc: 3
nt: 1
nz: 1
nlut: 1

What do you think?

As I mentioned in the other topic, this image was originally from a VSI image that I opened using QuPath and then exported a section to FIJI. I could try opening the VSI in Fiji directly, though this did not work for me previously…

Thanks!

Maria

1 Like

Hi @MariaZ,

Awesome, those details gave me an idea where the problem could be.
Would you mind trying the following:

  1. Delete your current bigwarp jar (a file that looks something like: Fiji.app/plugins/bigwarp_fiji-#.#.#.jar
  2. Download this patched version of bigwarp
  3. put the new file you just downloaded in Fiji.app/plugins
  4. Restart Fiji
  5. try running again with your images
  6. Tell me what happened!

I think it’s likely to work with this fix.

Thanks again for reporting this problem
John

Hello @bogovicj,

Thanks for your time looking into this, I did as you said and sadly I am still getting an error.

WARNING:
Opening <SpimData> dataset that is not suited for interactive browsing.
Consider resaving as HDF5 for better performance.
WARNING:
Opening <SpimData> dataset that is not suited for interactive browsing.
Consider resaving as HDF5 for better performance.
Exception in thread "PainterThread" java.lang.ArrayIndexOutOfBoundsException: 1

Here is an example of my image file (downsized 10x)
Image09 downsized 10x.tif (6.1 MB)

And a screenshot of the error, the tiff target image still has a grey screen.

I will start working on importing the VSI directly into FIJI and I will post again once I see what happens.

Thanks again,

Maria

Hello @bogovicj

Good news! I managed to open my VSI file in FIJI using BIOP VSI reader https://biop.epfl.ch/TOOL_VSI_Reader.html

Then I exported a brain section and saved at tiff and used Big Warp!

It seems to have worked! I am not sure why my Qupath exported tiff file was not working with Big Warp… however opening my VSI and generating my tiff in Fiji seems to have avoided the problem!!

Thank you for your time and help!! I really appreciate it! :blush:

Maria