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https://github.com/mmasoud1/histojs
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
https://github.com/mmasoud1/histojs
cell-cell-interaction cell-segmentation digital-slide-archive image-processing mibiscope multichannel multiplexed-imaging multiplexed-imaging-analysis ome-tiff phenotyping proteomics proteomics-data-analysis single-cell spatial-biology spatial-data-analysis whole-slide-imaging
Last synced: about 1 month ago
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HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
- Host: GitHub
- URL: https://github.com/mmasoud1/histojs
- Owner: Mmasoud1
- License: mit
- Created: 2020-12-17T22:21:42.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-02-29T14:38:53.000Z (10 months ago)
- Last Synced: 2024-02-29T15:39:59.679Z (10 months ago)
- Topics: cell-cell-interaction, cell-segmentation, digital-slide-archive, image-processing, mibiscope, multichannel, multiplexed-imaging, multiplexed-imaging-analysis, ome-tiff, phenotyping, proteomics, proteomics-data-analysis, single-cell, spatial-biology, spatial-data-analysis, whole-slide-imaging
- Language: JavaScript
- Homepage: https://mmasoud1.github.io/HistoJS/
- Size: 290 MB
- Stars: 10
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: docs/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: docs/CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
## HistoJS []() [](https://joss.theoj.org/papers/10.21105/joss.06317)
[]()
[](https://github.com/Mmasoud1/HistoJS/blob/main/LICENSE) []()[]()
[]()
**[Demo](https://mmasoud1.github.io/HistoJS)   [Updates](#Updates)   [Doc](https://github.com/mmasoud1/HistoJS/wiki/)   [News!](#News)**
HistoJS 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.
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.
## Live Demo
HistoJS [Demo](https://mmasoud1.github.io/HistoJS) hosted by Github pages shows most core functionalities.
The analysis mode needs running of the Flask RestAPIs as the steps described [here](https://github.com/Mmasoud1/HistoJS/wiki/Setup-Environment).
## News!
* 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.
* 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.
* HistoJS abstract is accepted for poster presentation in the [OHBM](https://www.humanbrainmapping.org/) 2024 Annual Meeting in Seoul, Korea.
## Citation
HistoJS [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) [](https://joss.theoj.org/papers/10.21105/joss.06317)
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
For **BibTeX** format that is used by some publishers, please use:
```BibTeX:
@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}
}
```
## Updates
https://github.com/Mmasoud1/HistoJS/assets/36082112/7598afb0-ef05-40e0-9d53-767fbc0e6d99
**HistoJS Design Mode (Data source: [Rashid et al](https://doi.org/10.7303/syn17865732))**
https://github.com/Mmasoud1/HistoJS/assets/36082112/7ba5c733-3b31-47e9-9cc4-e9fb606d42da
**HistoJS V1.0.0 Analysis Mode**
[](https://docs.google.com/forms/d/e/1FAIpQLSdHuO--mG00sKydQpJ7sPpDmhcJ4ECdj-wAB1kwXQExh_nUSg/viewform?usp=sf_link) [](https://github.com/Mmasoud1/HistoJS/blob/main/LICENSE)
**Mohamed Masoud - 2023**