{"id":21061839,"url":"https://github.com/mmasoud1/histojs","last_synced_at":"2025-10-15T16:10:58.684Z","repository":{"id":46713471,"uuid":"322426576","full_name":"Mmasoud1/HistoJS","owner":"Mmasoud1","description":"HistoJS: Web-Based Analytical Tool for Multiplexed Images. 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HistoJS provides open-source and extensible tools for analyzing spatial-molecular patterns, offering a deeper understanding of single-cell spatial relationships. It also features machine learning algorithms in a user-friendly interactive interface for the biomedical community.\n \u003c/p\u003e\n\n \u003cp align=\"justify\"\u003e\nThe tool can manage, store, and analyze the multi-channel OME-Tiff files using  Digital Slide Archive as a backbone to update the image metadata remotely or locally.\n \u003c/p\u003e\n\n\n## Live Demo\n\nHistoJS [Demo](https://mmasoud1.github.io/HistoJS) hosted by Github pages shows most core functionalities.  \n\nThe analysis mode needs running of the Flask RestAPIs as the steps described [here](https://github.com/Mmasoud1/HistoJS/wiki/Setup-Environment).\n\n\n## News!\n\n* HistoJS abstract is accepted for poster presentation in the  SIAM 2024 Conference on Imaging Science ([IS24](https://www.siam.org/conferences/cm/conference/is24)) in Atlanta, GA.\n\n\u003cdiv align=\"center\"\u003e\n   \u003cimg src=\"https://github.com/Mmasoud1/HistoJS/blob/main/Demo/News/IS24.png\"  width=\"40%\"\u003e\n\u003c/div\u003e\n\n\u003cbr\u003e\n\n* HistoJS [paper](https://joss.theoj.org/papers/10.21105/joss.06317) is published in the Journal of Open Source Software (JOSS) on Feb 07, 2024.\n\n\u003cdiv align=\"center\"\u003e\n   \u003ca href=\"https://joss.theoj.org/papers/10.21105/joss.06317\"\u003e\u003cimg src=\"https://github.com/Mmasoud1/HistoJS/blob/main/Demo/News/JOSS_Logo.png\"\u003e\u003c/a\u003e\n\u003c/div\u003e\n\n\u003cbr\u003e\n\n* HistoJS abstract is accepted for poster presentation in the [OHBM](https://www.humanbrainmapping.org/) 2024 Annual Meeting in Seoul, Korea.\n\n\u003cdiv align=\"center\"\u003e\n   \u003cimg src=\"https://github.com/Mmasoud1/HistoJS/blob/main/Demo/News/OHBM_2024.png\"  width=\"40%\"\u003e\n\u003c/div\u003e\n\n\u003cbr\u003e\n\n## Citation\n\nHistoJS [paper](https://joss.theoj.org/papers/10.21105/joss.06317) for v1.1.0 is published on Feb 07, 2024, in the Journal of Open Source Software (JOSS) [![DOI](https://joss.theoj.org/papers/10.21105/joss.06317/status.svg)](https://joss.theoj.org/papers/10.21105/joss.06317) \n\n\n\u003cbr\u003e\n\nFor **APA** style, the paper can be **cited** as: \n\n\u003e Masoud, M., Gutman, D., \u0026 Plis, S. (2024). HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images. Journal of Open Source Software, 9(94), 6317. https://doi.org/10.21105/joss.06317\n\n\u003cbr\u003e\n\nFor **BibTeX** format that is used by some publishers,  please use: \n\n```BibTeX: \n@article{Masoud_HistoJS_Web-Based_Analytical_2024,\n   author = {Masoud, Mohamed and Gutman, David and Plis, Sergey},\n   doi = {10.21105/joss.06317},\n   journal = {Journal of Open Source Software},\n   month = feb,\n   number = {94},\n   pages = {6317},\n   title = {{HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images}},\n   url = {https://joss.theoj.org/papers/10.21105/joss.06317},\n   volume = {9},\n   year = {2024}\n}\n```\n\n\u003cbr\u003e\n\n## Updates\n\n\u003cdiv align=\"center\"\u003e\n\nhttps://github.com/Mmasoud1/HistoJS/assets/36082112/7598afb0-ef05-40e0-9d53-767fbc0e6d99\n\n**HistoJS Design Mode (Data source: [Rashid et al](https://doi.org/10.7303/syn17865732))**\n\u003c/div\u003e\n\n\u003cbr\u003e\n\n\u003cdiv align=\"center\"\u003e\n\n\u003c!-- https://github.com/Mmasoud1/HistoJS/assets/36082112/95499746-8d97-4d9a-97e1-2ee12d3516d6   --\u003e\nhttps://github.com/Mmasoud1/HistoJS/assets/36082112/7ba5c733-3b31-47e9-9cc4-e9fb606d42da  \n\n\u003c!-- ![Interface](https://github.com/mmasoud1/HistoJS/blob/main/Demo/AnalysisMode.gif) --\u003e\n\n**HistoJS V1.0.0 Analysis Mode**\n\u003c/div\u003e\n\n\n\u003cbr\u003e\n\n\n\n\u003cdiv align=\"center\"\u003e\n\n[![Google Doc](https://img.shields.io/badge/HistoJS-Feedback-blue)](https://docs.google.com/forms/d/e/1FAIpQLSdHuO--mG00sKydQpJ7sPpDmhcJ4ECdj-wAB1kwXQExh_nUSg/viewform?usp=sf_link) [![MIT-License ](https://img.shields.io/badge/license-MIT-green)](https://github.com/Mmasoud1/HistoJS/blob/main/LICENSE)\n\n**Mohamed Masoud - 2023**\n\u003c/div\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmmasoud1%2Fhistojs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmmasoud1%2Fhistojs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmmasoud1%2Fhistojs/lists"}