BigDataViewer BDV VoxelSize and other metadata


I converted large files to xml/H5 bigdataviewer format. Somehow the voxelSize and time step got messed up. After a while looking at the xml file I found that i need to change the Affine transformation part for every time points.


    <ViewRegistration timepoint="0" setup="1">
      <ViewTransform type="affine">
        <affine>1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0</affine>


    <ViewRegistration timepoint="0" setup="1">
      <ViewTransform type="affine">
        <affine>0.173 0.0 0.0 0.0 0.0 0.173 0.0 0.0 0.0 0.0 2.0 0.0</affine>

Is there a simpler way? for instance specify the properties of the image within the UI (like in imageJ1) and just re-save the xml? Does the VoxelSize entry has any effect on the rendering of the image?

Also where can one specify the time-interval in the xml file?



the Multiview Reconstruction Application has a tool for that:

Fiji > Plugins > Multiview Reconstruction > Batch Processing > Tools > Specify Calibration
Load the xml and then click ok.

The BigStitcher for sure has also a way to change that. I guess via calling up the menu with right click on the dataset.

I don’t think it is strictly necessary to specify the timeresolution. At least for the multiview reconstruction it would have no influence.


Thanks it worked out. From my naive approach I would have expected it in the BDV as an option. One opens a file and realizes that the calibration is wrong and wants to fix it.
I have the impression that there is no deltaT entry in the xml.

I don’t think that the time resolution is used anywhere in the BigDataViewer or associated programs, for a timestamp for example.

If you want to you can add a tag in the .xml yourself. As long as you preserve the .xml format I guess you will not break anything, at least that is the point of the xml. Here for example:

    <Timepoints type="range">

Or in the channel information…
But otherwise the metadata is not really preserved…