{"id":21608160,"url":"https://github.com/thennen/counting-molecules","last_synced_at":"2026-01-25T01:03:01.902Z","repository":{"id":43468984,"uuid":"141155345","full_name":"thennen/counting-molecules","owner":"thennen","description":"Automates counting and categorization of molecules in scanning probe microscopy images","archived":false,"fork":false,"pushed_at":"2024-09-02T08:06:48.000Z","size":1703,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-11T04:37:15.774Z","etag":null,"topics":["cluster-analysis","computer-vision","image-analysis","microscopy","molecules","zernike-moments"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/thennen.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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,"zenodo":null}},"created_at":"2018-07-16T15:09:10.000Z","updated_at":"2024-09-11T12:18:36.000Z","dependencies_parsed_at":"2024-11-24T20:36:51.074Z","dependency_job_id":"6bc10e9a-abe8-48c4-b1d3-290d48e896ec","html_url":"https://github.com/thennen/counting-molecules","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/thennen/counting-molecules","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thennen%2Fcounting-molecules","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thennen%2Fcounting-molecules/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thennen%2Fcounting-molecules/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thennen%2Fcounting-molecules/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/thennen","download_url":"https://codeload.github.com/thennen/counting-molecules/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/thennen%2Fcounting-molecules/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28740399,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-24T22:12:27.248Z","status":"ssl_error","status_checked_at":"2026-01-24T22:12:10.529Z","response_time":89,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":["cluster-analysis","computer-vision","image-analysis","microscopy","molecules","zernike-moments"],"created_at":"2024-11-24T20:36:42.323Z","updated_at":"2026-01-25T01:03:01.883Z","avatar_url":"https://github.com/thennen.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# counting-molecules\n\n[![DOI](https://zenodo.org/badge/141155345.svg)](https://zenodo.org/badge/latestdoi/141155345)\n\nThis project contains a set of functions to automate the counting and categorization of molecules, and is specifically tailored for data generated from low temperature scanning probe microscopes.\n\n\u003cimg src=figure.png width=500\u003e\n\n\nWe described our approach in [Software Impacts](https://www.softwareimpacts.com/article/S2665-9638(22)00041-0/fulltext), and the code was also used to generate Fig. 3 of [this publication](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201812334).\n\n## Getting Started\n\nThis is a glorified script that makes use of existing python libraries.  Written in python 3+, if unsure, start by installing [Anaconda](https://www.anaconda.com/download).\n\n### Dependencies\n\n* [Python 3+](https://www.anaconda.com/download)\n* [SciPy](https://www.scipy.org/)\n* [NumPy](http://www.numpy.org/)\n* [Matplotlib](https://matplotlib.org/)\n* [matplotlib-scalebar](https://pypi.org/project/matplotlib-scalebar/)\n* [Scikit-image](https://scikit-image.org/)\n* [Scikit-learn](https://scikit-learn.org/stable/)\n* [Nanonispy](https://github.com/underchemist/nanonispy)\n* [Mahotas](https://mahotas.readthedocs.io/en/latest/)\n\n### Installing\n\nThis package is not yet registered. To install, clone this repository, navigate to its directory, and run:\n\n```\npip install .\n```\n\n### Examples\n\n`Helicene_example`, `APT_example` and `APT_2_example` are three example scripts that generate the figures in our [article](https://www.softwareimpacts.com/article/S2665-9638(22)00041-0/fulltext).\n\nSteps to reproduce:\n\n1. Download the data files from this [figshare repo](https://doi.org/10.6084/m9.figshare.19217556) into the examples folder.\n2. Run the individual script files in the examples folder to generate each figure.\n\n\n\n## Versioning\n\nWe use github, see the [tags on this repository](https://github.com/thennen/counting-molecules/tags)\n\n## Authors\n\n* **Jack Hellerstedt** [jhellerstedt](https://github.com/jhellerstedt)\n* **Tyler Hennen** [THennen](https://github.com/thennen)\n\n## License\n\nThis project is licensed under the MIT License.\n\n## Acknowledgements\n\nThis project was inspired by the need to analyze the data that eventually resulted in [this publication](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201812334).\nWe also made use of the data available from [this work.](https://www.nature.com/articles/nchem.2662)\nThis happened at the [Nanosurf lab.](https://nanosurf.fzu.cz/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthennen%2Fcounting-molecules","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthennen%2Fcounting-molecules","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthennen%2Fcounting-molecules/lists"}