Python + BigVolumeViewer

See thread here for description of use case and end goals Imglyb + BigDataViewer.

To a similar end, I am exploring real time visualization of our data using BigVolumeViewer through Python. The code below does work (a viewing window pops up displaying the volume - awesome!).

A few questions about current functionality are:

  1. Is it possible to open a BigStitcher style H5 file with BVV? In essence a single H5 file containing multiple image volumes, with positions specified in an XML file?

  2. If not, is it possible to add multiple volumes to a single BVV instance?

Thank you!

Working code

import scyjava_config
import imglyb
import imglyb.util as util
from jnius import autoclass, PythonJavaClass, java_method, cast
import time
import numpy as np

xmlFilename = 'X:\\test1\\data-f0.xml'

spimData = autoclass('bdv.spimdata.SpimDataMinimal')
spimXML = autoclass('bdv.spimdata.XmlIoSpimDataMinimal')

spimData = spimXML().load(xmlFilename)
BvvStackSource = autoclass('bvv.util.BvvStackSource')
BvvFunctions = autoclass('bvv.util.BvvFunctions')
BvvStackSource =


Just a heads up that we did a mini hackathon at Janelia last week, and we have a python wrapper of sciview (which delivers bvv) in testing now. So this will provide BDV-style volumes + annotations, meshes, and all the other goodness that comes from scenery/SciView. We’re just ironing out the API then will make the repo public.


Thanks for the update. We will be very interested in this. Looking forward to seeing the release!

It will enable annotations of BDV volumes? This is something we have been interested in for a while now!