BigStitcher loading tiles from hdf5

Hi everyone,

Is there a possibility to define a BigSticher project from several HDF5 files that were created beforehand by BigStitcher?
In workflows where you want to nest output of a project in a new project, this functionality would save a lot of time. My current workaround is
(1) export to tiff
(2) create new project in BigStitcher with Tiff files and
(3) convert tiff files into HDF5.

Thanks a lot to @hoerldavid and @StephanPreibisch for their great work!

Best Moritz

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Hello Moritz,

In the bigdataviewer core repository there is a class called MergeExample

This sounds like what you might be after.

I have tried to implement this using beanshell scripting in the script editor similar to as described in the bigwarp examples found here:

Unfortunately, I have not been able to get it to work.
Unlike the bigwarp classes in this above example, for some reason I have not been able to access the inner class of MergeExample.



Hello Adam,

thank you very much for the info! I will have a look!


Hello Moritz,

I would like to load pre-converted multi-resolution HDF5 files (BigDataViewer format) as BigStitcher tiles, which is similar to what you wanted to perform. Have you managed?

Alternatively I would already be happy to perform TIF to HDF5 conversion from BigStitcher but I do not think that it can load TIF files as virtual stack, hence this solution is pretty limited for huge datasets.


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