cselab / stitch

A scalable implementation of WobblyStitcher for 3D microscopy images

WobblyStitcher

Introduction

A scalable implementation of WobblyStitcher

Dependencies

$ python3 -m pip install --no-deps numpy scikit-image scipy

Install

$ make

Visualization

ImageJ

Getting started

Generate four files with fake input

$ (cd tool && make)
$ tool/gen -p 1 -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
391x391x200le.raw
391x391.pgm

Open 391x391x200le.raw in ImageJ.

Similar programs

BigStitcher
TeraStitcher
ClearMap

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.