https://github.com/cselab/stitch

A scalable implementation of WobblyStitcher for 3D microscopy images
https://github.com/cselab/stitch

3d-images image-analysis medical-imaging microscopy-images multiprocessing numpy parallel python segmentation-pipeline visualization

Last synced: about 1 month ago
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A scalable implementation of WobblyStitcher for 3D microscopy images

• Host: GitHub
• URL: https://github.com/cselab/stitch
• Owner: cselab
• License: gpl-3.0
• Created: 2021-08-20T15:24:15.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2022-09-14T01:18:40.000Z (over 3 years ago)
• Last Synced: 2023-03-23T22:11:00.945Z (about 3 years ago)
• Topics: 3d-images, image-analysis, medical-imaging, microscopy-images, multiprocessing, numpy, parallel, python, segmentation-pipeline, visualization
• Language: Python
• Homepage:
• Size: 175 KB
• Stars: 8
• Watchers: 4
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
WobblyStitcher


Introduction
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 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

387x387x203le.raw

387x387.pgm



Open 387x387x203le.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.