{"id":19400994,"url":"https://github.com/google-research/sofima","last_synced_at":"2025-04-05T22:03:31.639Z","repository":{"id":42485355,"uuid":"458165527","full_name":"google-research/sofima","owner":"google-research","description":"Scalable Optical Flow-based Image Montaging and Alignment","archived":false,"fork":false,"pushed_at":"2025-02-18T20:16:51.000Z","size":4961,"stargazers_count":68,"open_issues_count":7,"forks_count":16,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-03-29T21:02:50.490Z","etag":null,"topics":["2d","3d","4d","alignment-algorithm","biomedical-image-processing","connectomics","electron-microscopy","jax","microscopy","python3","stitching-algorithm"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/google-research.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/contributing.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-02-11T11:49:48.000Z","updated_at":"2025-03-25T14:13:32.000Z","dependencies_parsed_at":"2024-01-15T00:07:19.184Z","dependency_job_id":"2318a008-d0a3-4d38-9e5a-a180f6a1dc1a","html_url":"https://github.com/google-research/sofima","commit_stats":{"total_commits":73,"total_committers":6,"mean_commits":"12.166666666666666","dds":0.5205479452054795,"last_synced_commit":"c390d3ffc5c4aa09db428a8c59abc3e3a23de7b1"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/google-research%2Fsofima","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/google-research%2Fsofima/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/google-research%2Fsofima/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/google-research%2Fsofima/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/google-research","download_url":"https://codeload.github.com/google-research/sofima/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247406084,"owners_count":20933803,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["2d","3d","4d","alignment-algorithm","biomedical-image-processing","connectomics","electron-microscopy","jax","microscopy","python3","stitching-algorithm"],"created_at":"2024-11-10T11:16:34.218Z","updated_at":"2025-04-05T22:03:31.601Z","avatar_url":"https://github.com/google-research.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SOFIMA\n\nSOFIMA (Scalable Optical Flow-based Image Montaging and Alignment) is a tool\nfor stitching, aligning and warping large 2d, 3d and 4d microscopy datasets.\n\n[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)\n\nThis is not an officially supported Google product.\n\n# Installation\n\nSOFIMA is implemented purely in Python, and does not require a build step. To\ninstall it directly from the repository, run:\n\n```shell\n  pip install git+https://github.com/google-research/sofima\n```\n\n# Overview\n\nSOFIMA uses optical flow regularized with an elastic mesh to establish\nmaps between data in different coordinate systems. Both the [flow estimator](flow_field.py)\nas well as the [mesh solver](mesh.py) are implemented in [JAX](https://github.com/google/jax)\nand will automatically take advantage of GPU acceleration if the hardware if available.\n\nA core data structure used throughout the project is a *coordinate map* stored\nas a dense array of relative offsets (see the module docstring in [map_utils.py](map_utils.py)\nfor details). Among other uses, this is the representation of the estimated flow fields\nand the mesh node positions.\n\n# Example usage\n\n * [electron microscopy tile stitching](https://colab.research.google.com/github/google-research/sofima/blob/main/notebooks/em_stitching.ipynb)\n * [electron microscopy section alignment](https://colab.research.google.com/github/google-research/sofima/blob/main/notebooks/em_alignment.ipynb)\n\n# License\n\nLicensed under the Apache License, Version 2.0 (the \"License\");\nyou may not use this software except in compliance with the License.\nYou may obtain a copy of the License at \u003chttp://www.apache.org/licenses/LICENSE-2.0\u003e.\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgoogle-research%2Fsofima","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgoogle-research%2Fsofima","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgoogle-research%2Fsofima/lists"}