{"id":32177409,"url":"https://github.com/mehta-lab/waveorder","last_synced_at":"2026-02-04T18:03:21.828Z","repository":{"id":41127613,"uuid":"321525186","full_name":"mehta-lab/waveorder","owner":"mehta-lab","description":"Wave optical models and inverse algorithms for label-agnostic imaging of density \u0026 orientation.","archived":false,"fork":false,"pushed_at":"2026-01-30T00:46:14.000Z","size":165823,"stargazers_count":40,"open_issues_count":67,"forks_count":7,"subscribers_count":5,"default_branch":"main","last_synced_at":"2026-01-30T05:28:14.616Z","etag":null,"topics":["label-free","mipolscope","optics","permittivity","permittivity-tensor-imaging","phase","polarization","qlipp","reconstruction-algorithm","scattering","simulation"],"latest_commit_sha":null,"homepage":"https://waveorder.readthedocs.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mehta-lab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-12-15T02:02:08.000Z","updated_at":"2026-01-30T00:27:30.000Z","dependencies_parsed_at":"2024-04-23T22:27:21.388Z","dependency_job_id":"af0c894c-502a-47a4-bd25-4422156c387c","html_url":"https://github.com/mehta-lab/waveorder","commit_stats":{"total_commits":410,"total_committers":15,"mean_commits":"27.333333333333332","dds":0.6560975609756098,"last_synced_commit":"8f1f65c147c8ee1b9efb584b74460ba954e7f3bb"},"previous_names":[],"tags_count":19,"template":false,"template_full_name":null,"purl":"pkg:github/mehta-lab/waveorder","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mehta-lab%2Fwaveorder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mehta-lab%2Fwaveorder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mehta-lab%2Fwaveorder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mehta-lab%2Fwaveorder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mehta-lab","download_url":"https://codeload.github.com/mehta-lab/waveorder/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mehta-lab%2Fwaveorder/sbom","scorecard":{"id":635381,"data":{"date":"2025-08-11","repo":{"name":"github.com/mehta-lab/waveorder","commit":"0d3fe54e3123d2150b201a8683982a6ef7d517a4"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":5.6,"checks":[{"name":"Code-Review","score":7,"reason":"Found 11/15 approved changesets -- score normalized to 7","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Maintained","score":10,"reason":"7 commit(s) and 9 issue activity found in the last 90 days -- score normalized to 10","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/pr.yml:1","Warn: no topLevel permission defined: .github/workflows/test.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: BSD 3-Clause \"New\" or \"Revised\" License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pr.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/pr.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pr.yml:21: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/pr.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pr.yml:65: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/pr.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pr.yml:67: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/pr.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/test.yml:16: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/test.yml/main?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/test.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/test.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test.yml:24: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/test.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test.yml:40: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/test.yml/main?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/test.yml:45: update your workflow using https://app.stepsecurity.io/secureworkflow/mehta-lab/waveorder/test.yml/main?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/pr.yml:26","Warn: pipCommand not pinned by hash: .github/workflows/pr.yml:27","Warn: pipCommand not pinned by hash: .github/workflows/pr.yml:72","Warn: pipCommand not pinned by hash: .github/workflows/pr.yml:73","Warn: pipCommand not pinned by hash: .github/workflows/test.yml:35","Warn: pipCommand not pinned by hash: .github/workflows/test.yml:36","Info:   0 out of   6 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   3 third-party GitHubAction dependencies pinned","Info:   0 out of   6 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 30 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-21T09:01:57.879Z","repository_id":41127613,"created_at":"2025-08-21T09:01:57.879Z","updated_at":"2025-08-21T09:01:57.879Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29092734,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-04T03:31:03.593Z","status":"ssl_error","status_checked_at":"2026-02-04T03:29:50.742Z","response_time":62,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":["label-free","mipolscope","optics","permittivity","permittivity-tensor-imaging","phase","polarization","qlipp","reconstruction-algorithm","scattering","simulation"],"created_at":"2025-10-21T20:04:49.425Z","updated_at":"2026-02-04T18:03:21.818Z","avatar_url":"https://github.com/mehta-lab.png","language":"Python","readme":"\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/user-attachments/assets/00367e51-0e0a-445e-8d12-2a273f9014aa\" alt=\"Image\" width=\"50%\"\u003e\n\u003c/p\u003e\n\n[![Python package index](https://img.shields.io/pypi/v/waveorder.svg)](https://pypi.org/project/waveorder)\n[![PyPI monthly downloads](https://img.shields.io/pypi/dm/waveorder.svg)](https://pypistats.org/packages/waveorder)\n[![Total downloads](https://pepy.tech/badge/waveorder)](https://pepy.tech/project/waveorder)\n[![GitHub contributors](https://img.shields.io/github/contributors-anon/mehta-lab/waveorder)](https://github.com/mehta-lab/waveorder/graphs/contributors)\n![GitHub Repo stars](https://img.shields.io/github/stars/mehta-lab/waveorder)\n![GitHub forks](https://img.shields.io/github/forks/mehta-lab/waveorder)\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/waveorder)\n\nLabel-agnostic computational microscopy of architectural order.\n\n# Overview\n\n`waveorder` is a generalist framework for label-agnostic computational microscopy of architectural order, i.e., density, alignment, and orientation of biomolecules with the spatial resolution down to the diffraction limit. The framework implements wave-optical simulations and corresponding reconstruction algorithms for diverse label-free and fluorescence computational imaging methods that enable quantitative imaging of the architecture of dynamic cell systems.\n\nOur goal is to enable modular and user-friendly implementations of computational microscopy methods for dynamic imaging across the scales of organelles, cells, and tissues.\n\n\nThe framework is described in the following [preprint](https://arxiv.org/abs/2412.09775).\n\nhttps://github.com/user-attachments/assets/4f9969e5-94ce-4e08-9f30-68314a905db6\n\n\u003cdetails\u003e\n`waveorder` enables simulations and reconstructions of label-agnostic microscopy data as described in the following [preprint](https://arxiv.org/abs/2412.09775)\n\u003csummary\u003e Chandler et al. 2024 \u003c/summary\u003e\n\u003cpre\u003e\u003ccode\u003e\n@article{chandler_2024,\n    author = {Chandler, Talon and Hirata-Miyasaki, Eduardo and Ivanov, Ivan E. and Liu, Ziwen and Sundarraman, Deepika and Ryan, Allyson Quinn and Jacobo, Adrian and Balla, Keir and Mehta, Shalin B.},\n\ttitle = {waveOrder: generalist framework for label-agnostic computational microscopy},\n\tjournal = {arXiv},\n\tyear = {2024},\n\tmonth = dec,\n\teprint = {2412.09775},\n\tdoi = {10.48550/arXiv.2412.09775}\n}\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/details\u003e\n\n# Computational Microscopy Methods\n\n `waveorder` framework enables simulations and reconstructions of data for diverse one-photon (single-scattering based) computational microscopy methods, summarized below.\n\n## Label-free microscopy\n\n### Quantitative label-free imaging with phase and polarization (QLIPP)\n\nAcquisition, calibration, background correction, reconstruction, and applications of QLIPP are described in the following [E-Life Paper](https://elifesciences.org/articles/55502):\n\n[![Unveiling the invisible](https://github.com/mehta-lab/recOrder/blob/main/docs/images/comms_video_screenshot.png?raw=true)](https://www.youtube.com/watch?v=JEZAaPeZhck)\n\n\u003cdetails\u003e\n\u003csummary\u003e Guo et al. 2020 \u003c/summary\u003e\n\u003cpre\u003e\u003ccode\u003e\n@article{guo_2020,\n\tauthor = {Guo, Syuan-Ming and Yeh, Li-Hao and Folkesson, Jenny and Ivanov, Ivan E. and Krishnan, Anitha P. and Keefe, Matthew G. and Hashemi, Ezzat and Shin, David and Chhun, Bryant B. and Cho, Nathan H. and Leonetti, Manuel D. and Han, May H. and Nowakowski, Tomasz J. and Mehta, Shalin B.},\n\ttitle = {Revealing architectural order with quantitative label-free imaging and deep learning},\n\tjournal = {eLife},\n\tvolume = {9},\n\tpages = {e55502},\n\tyear = {2020},\n\tdoi = {10.7554/eLife.55502}\n}\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/details\u003e\n\n### Permittivity tensor imaging (PTI)\n\nPTI provides volumetric reconstructions of mean permittivity ($\\propto$ material density), differential permittivity ($\\propto$ material anisotropy), 3D orientation, and optic sign. The following figure summarizes PTI acquisition and reconstruction with a small optical section of the mouse brain tissue:\n\n![Data_flow](https://github.com/mehta-lab/waveorder/blob/main/readme.png?raw=true)\n\nThe acquisition, calibration, background correction, reconstruction, and applications of PTI are described in the following [paper](https://doi.org/10.1101/2020.12.15.422951) published in Nature Methods:\n\n\u003cdetails\u003e\n\u003csummary\u003e Yeh et al. 2024 \u003c/summary\u003e\n\u003cpre\u003e\u003ccode\u003e\n@article{yeh_2024,\n\tauthor = {Yeh, Li-Hao and Ivanov, Ivan E. and Chandler, Talon and Byrum, Janie R. and Chhun, Bryant B. and Guo, Syuan-Ming and Foltz, Cameron and Hashemi, Ezzat and Perez-Bermejo, Juan A. and Wang, Huijun and Yu, Yanhao and Kazansky, Peter G. and Conklin, Bruce R. and Han, May H. and Mehta, Shalin B.},\n\ttitle = {Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution},\n\tjournal = {Nature Methods},\n\tvolume = {21},\n\tnumber = {7},\n\tpages = {1257--1274},\n\tyear = {2024},\n\tmonth = jul,\n\tissn = {1548-7105},\n\tpublisher = {Nature Publishing Group},\n\tdoi = {10.1038/s41592-024-02291-w}\n}\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/details\u003e\n\n\n### Quantitative phase imaging (QPI) from defocus\n__phase__ from a volumetric brightfield acquisition ([2D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-54-28-8566)/[3D phase](https://www.osapublishing.org/ao/abstract.cfm?uri=ao-57-1-a205))\n\n![Image](https://github.com/user-attachments/assets/caf7714b-59ee-40bb-9ee4-f13db4feece6)\n\n\n\u003cdetails\u003e\n\u003csummary\u003e Jenkins and Gaylord 2015 (2D QPI from defocus) \u003c/summary\u003e\n\u003cpre\u003e\u003ccode\u003e\n\t@article{Jenkins:15,\n\tauthor = {Micah H. Jenkins and Thomas K. Gaylord},\n\tjournal = {Appl. Opt.},\n\tkeywords = {Phase retrieval; Partial coherence in imaging; Interferometric imaging ; Imaging systems; Microlens arrays; Optical transfer functions; Phase contrast; Spatial resolution; Three dimensional imaging},\n\tnumber = {28},\n\tpages = {8566--8579},\n\tpublisher = {Optica Publishing Group},\n\ttitle = {Quantitative phase microscopy via optimized inversion of the phase optical transfer function},\n\tvolume = {54},\n\tmonth = {Oct},\n\tyear = {2015},\n\turl = {https://opg.optica.org/ao/abstract.cfm?URI=ao-54-28-8566},\n\tdoi = {10.1364/AO.54.008566},\n}\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e Soto, Rodrigo, and Alieva 2018 (3D QPI from defocus) \u003c/summary\u003e\n\u003cpre\u003e\u003ccode\u003e\n@article{Soto:18,\nauthor = {Juan M. Soto and Jos\\'{e} A. Rodrigo and Tatiana Alieva},\njournal = {Appl. Opt.},\nkeywords = {Coherence and statistical optics; Image reconstruction techniques; Optical transfer functions; Optical inspection; Three-dimensional microscopy; Acoustooptic modulators; Illumination design; Inverse design; LED sources; Three dimensional imaging; Three dimensional reconstruction},\nnumber = {1},\npages = {A205--A214},\npublisher = {Optica Publishing Group},\ntitle = {Optical diffraction tomography with fully and partially coherent illumination in high numerical aperture label-free microscopy \\[Invited\\]},\nvolume = {57},\nmonth = {Jan},\nyear = {2018},\nurl = {https://opg.optica.org/ao/abstract.cfm?URI=ao-57-1-A205},\ndoi = {10.1364/AO.57.00A205},\n}\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/details\u003e\n\n### QPI with differential phase contrast\n __phase__ from differential phase contrast\n\n***Work in progress***\n\n* [2D](https://www.osapublishing.org/oe/fulltext.cfm?uri=oe-23-9-11394\u0026id=315599) DPC\n* [3D](https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-7-10-3940\u0026id=349951) DPC\n\n\n## Fluorescence microscopy\n\n### Widefield deconvolution microscopy\n__fluorescence density__ from a widefield volumetric fluorescence acquisition.\n\n\u003cdetails\u003e\n\u003csummary\u003e Swedlow 2013 \u003c/summary\u003e\n\u003cpre\u003e\u003ccode\u003e\n@article{Swedlow:13,\nauthor = {Swedlow, John R.},\njournal = {Methods Cell Biol.},\ntitle = {Quantitative fluorescence microscopy and image deconvolution},\nyear = {2013},\nvolume = {114},\npages = {407--26},\ndoi = {10.1016/B978-0-12-407761-4.00017-8}\n}\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/details\u003e\n\n### Oblique plane light-sheet microscopy\n__fluorescence density__ from oblique plane light-sheet microscopy.\n\n\u003cdetails\u003e\n\u003csummary\u003e Ivanov, Hirata-Miyasaki, Chandler et al. 2024 \u003c/summary\u003e\n\u003cpre\u003e\u003ccode\u003e\n@article{ivanov_2024,\nauthor = {Ivanov, Ivan E. and Hirata-Miyasaki, Eduardo and Chandler, Talon and Cheloor-Kovilakam, Rasmi and Liu, Ziwen and Pradeep, Soorya and Liu, Chad and Bhave, Madhura and Khadka, Sudip and Arias, Carolina and Leonetti, Manuel D. and Huang, Bo and Mehta, Shalin B.},\ntitle = {Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells},\njournal = {PNAS Nexus},\nvolume = {3},\nnumber = {9},\npages = {pgae323},\nyear = {2024},\ndoi = {10.1093/pnasnexus/pgae323}\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/details\u003e\n\n\n## Citation\n\nPlease cite this repository, along with the relevant publications and preprints, if you use or adapt this code. The citation information can be found by clicking \"Cite this repository\" button in the About section in the right sidebar.\n\n## Installation\n\nCreate a virtual environment:\n\n```sh\nconda create -y -n waveorder python=3.12\nconda activate waveorder\n```\n\nMost users should install `waveorder` with:\n```sh\npip install waveorder[visual]\n```\n\nWe also maintain three dependency sets for different interfaces:\n\n```sh\npip install waveorder          # API, CLI\npip install waveorder[visual]  # API, CLI, GUI\npip install waveorder[all]     # API, CLI, GUI, docs, dev dependencies\n```\n\n\n\n(M1 users) `pytorch` has [incomplete GPU support](https://github.com/pytorch/pytorch/issues/77764),\nso please use `export PYTORCH_ENABLE_MPS_FALLBACK=1`\nto allow some operators to fallback to CPU if you plan to use GPU acceleration for polarization reconstruction.\n\n\n## Examples\nThe [examples](https://github.com/mehta-lab/waveorder/tree/main/docs/examples) illustrate simulations and reconstruction for 2D QLIPP, 3D phase from brightfield, and 2D/3D PTI methods. To run examples, use\n\n```sh\ngit clone https://github.com/mehta-lab/waveorder.git\ncd waveorder\npip install -e .[all]\npython ./docs/examples/models/phase_thick_3d.py\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmehta-lab%2Fwaveorder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmehta-lab%2Fwaveorder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmehta-lab%2Fwaveorder/lists"}