Saving RandomAccessibleInterval as bigdataviewer hdf5

bigdataviewer

#1

@bogovicj @hoerldavid @tpietzsch @joshmoore

Hello :slight_smile:

Is there somewhere code to write a 3D RAI to a bdv.h5 file?

It would be cool if that code was somewhat optimized for speed, but I guess within the limitations of hdf5 this is difficult to achieve. If there is already something stable I would also consider testing n5. I just have to be able to load the files as resolution-pyramids to be displayed within BigDataViewer, so currently I guess this means as SpimData.


#2

…meanwhile I modified the existing code to save an ImagePlus such that it accepts an RAI instead:


#3

Hi @Christian_Tischer,

Missed this until now. Thanks for making that modification.

Maybe too late to be helpful, but to go from an RAI to N5 use this.

It’s not multiscale, unfortunately.
At the Ostrava hackathon, I put together a multiscale N5 exporter. It’s not carefully tested yet though. Install this branch to your fiji to get it working. If you or anyone wants to try, please let me know.

John


#4

@bogovicj @joshmoore

FYI: I made a new version that can export a 5D XYZCT RAI: