{"id":49585615,"url":"https://github.com/cselab/stitch","last_synced_at":"2026-05-03T22:30:54.459Z","repository":{"id":47528077,"uuid":"398319765","full_name":"cselab/stitch","owner":"cselab","description":"A scalable implementation of WobblyStitcher for 3D microscopy 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["3d-images","image-analysis","medical-imaging","microscopy-images","multiprocessing","numpy","parallel","python","segmentation-pipeline","visualization"],"created_at":"2026-05-03T22:30:53.641Z","updated_at":"2026-05-03T22:30:54.452Z","avatar_url":"https://github.com/cselab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ch1\u003eWobblyStitcher\u003c/h1\u003e\n\n\u003ch2\u003eIntroduction\u003c/h2\n\nA scalable implementation\nof \u003ca href=\"https://christophkirst.github.io/ClearMap2Documentation/html/wobblystitcher.html#wobblystitcher\"\u003eWobblyStitcher\u003c/a\u003e\n\n\u003ch2\u003eDependencies\u003c/h2\u003e\n\n\u003cpre\u003e\n$ python3 -m pip install --no-deps numpy scikit-image scipy\n\u003c/pre\u003e\n\n\u003ch2\u003eInstall\u003c/h2\u003e\n\n\u003cpre\u003e\n$ make\n\u003c/pre\u003e\n\n\u003ch2\u003eVisualization\u003c/h2\u003e\n\n\u003ca href=\"https://imagej.nih.gov\"\u003eImageJ\u003c/a\u003e\n\n\u003ch2\u003eGetting started\u003c/h2\u003e\n\nGenerate four files with fake input\n\u003cpre\u003e\n$ (cd tool \u0026\u0026 make)\n$ tool/gen -p 1 -n 200 200 200 -o 15 15\n$ ls -1 *.raw\n200x200x200le.00.00.raw\n200x200x200le.00.01.raw\n200x200x200le.01.00.raw\n200x200x200le.01.01.raw\n\u003c/pre\u003e\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"img/input.png\" alt=\"fake input\"/\u003e\u003c/p\u003e\n\nstitch\n\u003cpre\u003e\n$ python3 main.py\nmain.py: processes = 4\n387x387x203le.raw\n387x387.pgm\n\u003c/pre\u003e\n\nOpen \u003ctt\u003e387x387x203le.raw\u003c/tt\u003e in ImageJ.\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"img/sample.png\" alt=\"sample output\"/\u003e\u003c/p\u003e\n\n\u003ch2\u003eSimilar programs\u003c/h2\u003e\n\n\u003ca href=\"https://imagej.net/plugins/bigstitcher\"\u003eBigStitcher\u003c/a\u003e\u003c/br\u003e\n\u003ca href=\"https://abria.github.io/TeraStitcher\"\u003eTeraStitcher\u003c/a\u003e\u003c/br\u003e\n\u003ca href=\"https://clearanatomics.github.io/ClearMapDocumentation\"\u003eClearMap\u003c/a\u003e\n\n\u003ch2\u003eReferences\u003c/h2\u003e\n\n1. Kirst, C., Skriabine, S., Vieites-Prado, A., Topilko, T., Bertin,\nP., Gerschenfeld, G., ... \u0026 Renier, N. (2020). Mapping the fine-scale\norganization and plasticity of the brain vasculature. Cell, 180(4),\n780-795.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcselab%2Fstitch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcselab%2Fstitch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcselab%2Fstitch/lists"}