HistoJS

HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images - Published in JOSS (2024)

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 14 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

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: 6 months ago · JSON representation ·

Repository

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

Basic Info

Host: GitHub
Owner: Mmasoud1
License: mit
Language: JavaScript
Default Branch: main
Homepage: https://mmasoud1.github.io/HistoJS/
Size: 290 MB

Statistics

Stars: 23
Watchers: 1
Forks: 2
Open Issues: 0
Releases: 2

Topics

Created about 5 years ago · Last pushed almost 2 years ago

Metadata Files

Readme Contributing License Code of conduct Citation

README.md

HistoJS

[![HistoJS logo](https://lh3.googleusercontent.com/Q3eYJfpQMety3sUUTLKeZKLkJBzx-NmLZNn1NphdWs9hBNYmfHCzZTphddpXDcfUxjtaHTXTr89R57LieZflqUsGHM3TxtIbVNoQOKf3ZbPjB01C8gYANmezAzq4JgUU=w1823)]() [![MIT-License ](https://img.shields.io/badge/license-MIT-green)](https://github.com/Mmasoud1/HistoJS/blob/main/LICENSE) [![Python ](https://img.shields.io/badge/python-3.5%20%7C%203.6%20%7C%203.7-blue)]()[![JS ](https://img.shields.io/badge/Types-JavaScript-blue)]() [![HW ](https://img.shields.io/badge/HardWare-GPU-green)]() **[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 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.

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

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

Citation

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

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**

[![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) **Mohamed Masoud - 2023**

Owner

Name: Mohamed E. Masoud
Login: Mmasoud1
Kind: user

Twitter: MMasoud2021
Repositories: 3
Profile: https://github.com/Mmasoud1

mmasoud2@outlook.com

JOSS Publication

HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images

Published

February 07, 2024

DOI

10.21105/joss.06317

Volume 9, Issue 94, Page 6317

Authors

Mohamed Masoud

David Gutman

Department of Pathology, Emory University School of Medicine, Atlanta, United States of America

Sergey Plis

Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, United States of America, Department of Computer Science, Georgia State University, Atlanta, United States of America

Editor

Beatriz Costa Gomes

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Masoud
  given-names: Mohamed
  orcid: "https://orcid.org/0000-0002-5365-242X"
- family-names: Gutman
  given-names: David
  orcid: "https://orcid.org/0000-0002-1386-8701"
- family-names: Plis
  given-names: Sergey
  orcid: "https://orcid.org/0000-0003-0040-0365"
contact:
- family-names: Masoud
  given-names: Mohamed
  orcid: "https://orcid.org/0000-0002-5365-242X"
doi: 10.5281/zenodo.10626533
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Masoud
    given-names: Mohamed
    orcid: "https://orcid.org/0000-0002-5365-242X"
  - family-names: Gutman
    given-names: David
    orcid: "https://orcid.org/0000-0002-1386-8701"
  - family-names: Plis
    given-names: Sergey
    orcid: "https://orcid.org/0000-0003-0040-0365"
  date-published: 2024-02-07
  doi: 10.21105/joss.06317
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6317
  title: "HistoJS: Web-Based Analytical Tool for Advancing Multiplexed
    Images"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06317"
  volume: 9
title: "HistoJS: Web-Based Analytical Tool for Advancing Multiplexed
  Images"

GitHub Events

Total

Watch event: 4
Fork event: 1

Last Year

Watch event: 4
Fork event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 168
Total Committers: 1
Avg Commits per committer: 168.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
mmasoud1	m**2@o**m	168

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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css/Metro-UI-CSS-master/package.json npm

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js/libs/webix/package.json npm

css/Metro-UI-CSS-master/metro.nuspec nuget

HistoJS

Science Score: 98.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

HistoJS

Live Demo

News!

Citation

Updates

Owner

JOSS Publication

HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

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Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

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