BigStitcher export fused as h5/xml doesn't work

imagej
hdf5
big-stitcher

#1

First of all I wish to thank @StephanPreibisch for this (and other) fantastic plugins! I realize this plugin is still in beta, but its already amazing!

I was successfully using it to pre-process, stitch and fuse a Zeiss Lightsheet Z1 dataset.

Fuse & export of the stitched dataset as tif was successful, but export as new h5/xml did not complete. It was more free RAM available than the estimated amount necessary and the BigStitcher was updated today.

After pressing OK the CPU load went up and the RAM filled, but after waiting nothing else happened as far as I could tell, see screenshot and console output below.

Exception in thread "Thread-8" java.lang.OutOfMemoryError: Java heap space
	at bdv.export.ProposeMipmaps.proposeMipmaps(ProposeMipmaps.java:93)
	at net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5.proposeMipmaps(Resave_HDF5.java:144)
	at net.preibisch.mvrecon.process.export.ExportSpimData2HDF5.queryParameters(ExportSpimData2HDF5.java:128)
	at net.preibisch.mvrecon.fiji.plugin.Image_Fusion.fuse(Image_Fusion.java:111)
	at net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FusionPopup$MyActionListener$1.run(FusionPopup.java:82)
	at java.lang.Thread.run(Thread.java:745)

For my understanding: is this function writing a new .h5/xml file? So far there is no dialogue as to where the file could be written to.


#2

@StephanPreibisch can you comment on this?


#3

Hi, we have not tested that well, I think it might just be that the HDF5 export loads everything into RAM first. I will have to check that. Thanks for reporting…but maybe it is a much simpler bug


#4

@StephanPreibisch thanks for your reply! I really like the BigStitcher already and am keen on using it. So if you have any updates to be tested, I’d be happy to help!


#5

Ok, I am almost there … I will update it tomorrow and it should work. There were just some smaller bugs, one remaining…


#6

It is fixed, tested and uploaded to the BigStitcher update site. Just update your Fiji and you should be good to go! All the best, Stephan


#7

thanks @StephanPreibisch! I just tested it on my side and is working like a charm.
Its really an awesome tool, thank you very much!

update: I just noticed that the voxel size is lost after exporting a fused h5 (also when exporting as tiff).