BigStitcher Transforms

Hi all,
Has anybody got any tips on BitStitcher? I’m trying to open a series of SPIM volumes from 8 different angles. To get started I:

  • create new dataset using bioformats opener
  • select the option to offset based on the metadata

[Aside - I’ve noticed that changing the name of .ome.tif files in Explorer is not advisable as it makes the files not behave as they should. The metadata on opening appears to be linked to the filename]

In BigDataViewer I see this really cool ring of spheroids that nicely illustrates that the spheroid is off axis. It does not rotate the volumes, but I assume that’s not in the metadata in a useful way given the picard twister is not in degrees.

[Aside - would love to know how to ‘lock in’ the colors; each time I touch anything it goes back to greyscale]

I’ve tried the option of applying transforms (with the option to remove all previous transforms) that apply a rotation, but it rotates them all by a single angle, and I need a cumulative angle for each in the series. Would love to know if that’s an option as I think that might be the best starting place.

I see in the metadata of the dataset.xml that there’s a section with transformations, and I was thinking about simply editing that with python or something to override presets.

I’ve tried manual transformations, as Stephan details in the cool bitsized YouTubes here for example:, but I can’t translate in the viewed orientation, and I end up making a mess by rotating in all axes. I’m not sure if it’s modifier (Ctrl, Shift etc) or it’s that he’s using Stitching, not Multiview.

All the above being said, does anybody know of other 3D fusion software or libraries that are worth trying?