A scalable implementation of WobblyStitcher for 3D microscopy images

WobblyStitcher

A scalable implementation of WobblyStitcher

Dependencies

$ python -m pip install numpy scipy scikit-image

Visualization

ImageJ

Getting started

Generate four files with fake input

$ (cd tool && make)
$ ./tool/gen -n 200 200 200 -o 10 10
$ ls -1 *.raw
200x200x200le.00.00.raw
200x200x200le.00.01.raw
200x200x200le.01.00.raw
200x200x200le.01.01.raw

stitch

$ python3 main.py
main.py: processes = 4
47% 390x390x200le.raw

Open 390x390x200le.raw in ImageJ.

References

1. Kirst, C., Skriabine, S., Vieites-Prado, A., Topilko, T., Bertin,
   P., Gerschenfeld, G., … & Renier, N. (2020). Mapping the fine-scale
   organization and plasticity of the brain vasculature. Cell, 180(4),
   780-795.

GitHub

https://github.com/cselab/stitch