Issue converting large Tiff file to XML/HDF5 using BigDataViewer / issue using Big Warp

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 onto a smaller Tiff image (size 2.2 MB ). However it is not working when I use my data file - a large tiff target image with three channels (637.5 MB). I am using FIJI 2.0 on MacOS, and the updated bigwarp_fiji-5.0.0.jar. The target window is blank grey (See picture) and I get this error message…

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

So now I am trying to convert the large tiff image into XML / HDF5 file. When I try using Big Data Viewer --> Export current image as xml/hdf5 — I get this error:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_202 [64-bit]; Mac OS X 10.14; 3692MB of 4524MB (81%)
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
 at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
 at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
 at ij.IJ.runPlugIn(IJ.java)
 at ij.Executer.runCommand(Executer.java:137)
 at ij.Executer.run(Executer.java:66)
 at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space
 at java.util.concurrent.FutureTask.report(FutureTask.java:122)
 at java.util.concurrent.FutureTask.get(FutureTask.java:192)
 at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:305)
 ... 5 more
Caused by: java.lang.OutOfMemoryError: Java heap space

Any suggestions? I would really appreciate it!

Thanks!

Maria

Hi @MariaZ

Welcome to the forum.

Sorry I’m just seeing this now. I’ll look into this soon…

John

Hello John!

No problem, I realize I didn’t use the tags BigWarp or BigDataViewer in this question and I wasn’t sure how to edit the post!

I did update FIJI just now and tried again and I am having the same error message

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

Thanks!

Maria

I now edited your post, adjusted the formatting a little, and added the #bigdataviewer and #bigwarp tags.

You can edit your own posts by clicking on the pencil icon Screenshot_2019-11-08%20Image%20sc%20Forum that you should find below each of your own posts.

1 Like

That doesn’t sound too big. It should be no problem.
How much memory do you give Fiji (menu Edit > Options > Memory & Threads …)?

The
Opening dataset that is not suited for interactive browsing.
Consider resaving as HDF5 for better performance.
is just a warning though. The
Exception in thread “PainterThread” java.lang.ArrayIndexOutOfBoundsException: 1
is likely unrelated, so I don’t know whether saving as HDF5 is even going to help.

2 Likes

Hello! Apparently the maximum memory I have given FIJI is 4311 MB.

I think you’re right that this warning might be unrelated.

I didn’t include this in my original post but the way I had generated the tiff image is by exporting a section of a virtual slide image file (VSI) from QuPath into ImageJ then saving it as a Tiff… Perhaps this is why @bogovicj you are unable to replicate the error?

This image is a screenshot of the VSI (top right there are the 6 brain sections) and I had selected one of the brain sections so I could open it in FIJI.