A scalable, out-of-memory, barebones implementation of WobblyStitcher
$ python3 -m pip install --no-deps numpy scikit-image scipy
$ make
Generate four files with fake input
$ (cd tool && make) $ tool/gen -p 1 -n 200 200 200 -o 15 15 $ 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 386x388x203le.raw 386x388.pgm
Open 386x388x203le.raw in ImageJ.
$ python3 main.py -h
usage: main.py [-h] [-n X Y Z] [-t X Y] [-o X Y] [-s X Y Z] [-m M] [-w A B]
[-p P] [-v]
[path ...]
stitch a grid of raw tiles
positional arguments:
path tiles in x-major order, default: output of tool/gen
options:
-h show this help message and exit
-n X Y Z tile size (default: 200 200 200)
-t X Y number of tiles (default: 2 2)
-o X Y overlap (default: 15 15)
-s X Y Z stride (default: 1 1 1)
-m M maximum shift (default: 20)
-w A B smoothing windows of shifts and wobble (default: 100 20)
-p P number of processes (default: 4)
-v verbose
Generate four tiles with vessels and a 30 pixel overlap. Every tile except the first wobbles in x and y along z.
$ tool/gen -p 3 -n 200 200 200 -o 30 30 -w 6 $ python3 main.py -o 30 30 -m 12 -w 10 6 $ python3 img.py img.py: img/wobble.xy.png img/merge.xy.png img.py: img/wobble.xz.png img/merge.xz.png
Center of the stitched volume where the four tiles meet: rigid alignment (left) and wobbly alignment (right). Top view
side view
ImageJ style merge: rigid in magenta, wobbly in green, white where they agree. Top view and side view
$ python3 -m pip install pytest $ python3 -m pytest
BigStitcher
TeraStitcher
ClearMap
- 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.