HistoJS

HistoJS

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Demo   Updates   Doc   News!

</div> <br> <img src="https://github.com/Mmasoud1/HistoJS/blob/main/css/logo/hisotjs_logo.svg" width="20%" align="right"> <p align="justify"> <b><a href="https://mmasoud1.github.io/HistoJS" style="text-decoration: none"> HistoJS</a></b> is a new web-based interactive tool designed to overcome the challenges of using highly-multiplexed immunofluorescence (HMIF) images for spatial biology research. 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. </p> <p align="justify"> The 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. </p>

Live Demo

HistoJS Demo hosted by Github pages shows most core functionalities.

The analysis mode needs running of the Flask RestAPIs as the steps described here.

News!

• HistoJS abstract is accepted for poster presentation in the SIAM 2024 Conference on Imaging Science (IS24) in Atlanta, GA.

<div align="center"> <img src="https://github.com/Mmasoud1/HistoJS/blob/main/Demo/News/IS24.png" width="40%"> </div> <br>

• HistoJS paper is published in the Journal of Open Source Software (JOSS) on Feb 07, 2024.

<div align="center"> <a href="https://joss.theoj.org/papers/10.21105/joss.06317"><img src="https://github.com/Mmasoud1/HistoJS/blob/main/Demo/News/JOSS_Logo.png"></a> </div> <br>

• HistoJS abstract is accepted for poster presentation in the OHBM 2024 Annual Meeting in Seoul, Korea.

<div align="center"> <img src="https://github.com/Mmasoud1/HistoJS/blob/main/Demo/News/OHBM_2024.png" width="40%"> </div> <br>

Citation

HistoJS paper for v1.1.0 is published on Feb 07, 2024, in the Journal of Open Source Software (JOSS)

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For APA style, the paper can be cited as:

Masoud, M., Gutman, D., & 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

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For BibTeX format that is used by some publishers, please use:

@article{Masoud_HistoJS_Web-Based_Analytical_2024,
   author = {Masoud, Mohamed and Gutman, David and Plis, Sergey},
   doi = {10.21105/joss.06317},
   journal = {Journal of Open Source Software},
   month = feb,
   number = {94},
   pages = {6317},
   title = {{HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images}},
   url = {https://joss.theoj.org/papers/10.21105/joss.06317},
   volume = {9},
   year = {2024}
}

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Updates

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https://github.com/Mmasoud1/HistoJS/assets/36082112/7598afb0-ef05-40e0-9d53-767fbc0e6d99

HistoJS Design Mode (Data source: Rashid et al)

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https://github.com/Mmasoud1/HistoJS/assets/36082112/7ba5c733-3b31-47e9-9cc4-e9fb606d42da

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HistoJS V1.0.0 Analysis Mode

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Mohamed Masoud - 2023

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