3d stitching

[bpavie]

Dear All,

I have a 3d stack that I would like to stitch using ashlar:
tile_x001_y001_z001.tif
tile_x001_y001_z002.tif
...
tile_x002_y010_z402.tif

I looked at the documentation but I am not sure exactly how I could use file pattern in x/y/z to stitch.
The filepattern seems to support cols and rows bu not Z stack.

Would it be possible to have a example on how to perform this or to know if it's possible to stitch 3d Z-stack with ashlar ?

Best,
Benjamin

[jmuhlich]

There's no support for stitching with Z-stack images. We have a few ideas for how it might be done but there are actually a lot of subtle issues to consider. You could try to stitch a fixed central Z-plane e.g. z200 in your case and see how the image looks -- use something like "filepattern|...|pattern=tile_x{col:03}_y{row:03}_z200.tif|...". If it works, I can show you how to generate a CSV with the corrected tile coordinates to use in reconstructing the full Z-stacks. Let me know if the stitching looks wrong and we can troubleshoot it.

[BioinfoTongLI]

Hi there, thanks for the great tool! I've been testing it and the results is surprising good for 2d tiles.
We're now also wondering if 3D is supported. And it seems to be a no?
If we'd like to make a PR, would you mind pointing me to the direction of where we should start?