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‎README.md

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[![HistoJS logo](https://lh3.googleusercontent.com/Q3eYJfpQMety3sUUTLKeZKLkJBzx-NmLZNn1NphdWs9hBNYmfHCzZTphddpXDcfUxjtaHTXTr89R57LieZflqUsGHM3TxtIbVNoQOKf3ZbPjB01C8gYANmezAzq4JgUU=w1823)]()
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[![Github contributors](https://img.shields.io/badge/contributors-*-brightgreen)](https://github.com/Mmasoud1/HistoJS/graphs/contributors) [![licence ](https://img.shields.io/badge/license-BY--NC--ND-orange)](https://creativecommons.org/licenses/by-nc-nd/3.0/) [![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)]()
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[![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)]()
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[![HW ](https://img.shields.io/badge/HardWare-GPU-green)]()
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The tool is using Digital Slide Archive as a backbone to update the image metadata remotely or locally.
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- Install requirements
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```bash
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3.4 < python < 3.8 is recommended
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```
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```bash
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conda env create -f histojs.yml
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```
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After creating the histojs environment, from the root level of the repository open a new terminal, activate the env and run the python ResApi file:
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```bash
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source activate histojs
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python RestApi.py
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```
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To run the localhost in the browser, just start up a simple local server from the root level of the repository with any available port number 8xxx (e.g. 8020)
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```bash
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python -m http.server 8xxx
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```
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-In the browser url type:
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```bash
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http://localhost:8020/
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```
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A dockerized version will be released soon for the api.
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For using the backbone DSA server, you need to create a user account on any DSA servers and upload your OME image, cells mask, and channels metadata CSV file to your collection as in this link:
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```bash
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https://styx.neurology.emory.edu/girder/#folder/5e361c5c34679044bda81b11
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```
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Please note: if the name of the OME image file is $fileName$.ome.tif (e.g. TONSIL-1_40X.ome.tif), the cell mask must be $fileName$_cellMask.tiff (e.g. TONSIL-1_40X_cellMask.tiff), and the Channel metadata CSV file should be $fileName$_channel_metadata.csv (e.g. TONSIL-1_40X_channel_metadata.csv)
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The Channel metadata CSV file must have at least two columns: 'channel_number' and 'channel_name'
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## Offline Demo
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<div align="center">
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[![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)[![CC BY-NC-ND ](https://img.shields.io/badge/license-BY--NC--ND-orange)](https://creativecommons.org/licenses/by-nc-nd/3.0/)
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[![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)
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**Copyright 2021 Mohamed Masoud**
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**Copyright 2023 Mohamed Masoud**
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</div>
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‎docs/CONTRIBUTING.md

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Thank you for taking the time to contribute to Brainchop!.
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Welcome again to HistoJS, and thank you for taking the time to contribute!
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The following is our set of guidelines to ease your contribution.
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#### Table Of Contents
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[Code of Conduct](#code-of-conduct)
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[Having a Question](#Having-a-question)
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[ Project Structure ](#Project-Structure)
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[How To Contribute?](#how-can-i-contribute)
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* [Reporting Bugs](#reporting-bugs)
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* [Suggesting Enhancements](#suggesting-enhancements)
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* [Your First Code Contribution](#your-first-code-contribution)
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* [Pull Requests](#pull-requests)
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## Code of Conduct
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This project and everyone participating in it is governed by the [Code of Conduct](https://github.com/neuroneural/brainchop/wiki/CODE-OF-CONDUCT). By participating, you are expected to uphold this code. Please report unacceptable behavior to [brainchop@github.com](mailto:brainchop@github.com).
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This project and everyone participating in it is governed by the [Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [HistoJS@github.com](mailto:HistoJS@github.com).
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## Having a question?
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> **Note:** Please don't file an issue to ask a question. You'll get faster results by using the resources below.
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* [Brainchop Discussions Board](https://github.com/neuroneural/brainchop/discussions)
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* [Brainchop Q&A](https://github.com/neuroneural/brainchop/discussions/categories/q-a)
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* [HistoJS Discussions Board](https://github.com/HistoJS/HistoJS/discussions)
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* [HistoJS FAQ](wiki/faq/)
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## Project Structure
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### Project Structure
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* **Root**
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* style
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* lib
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* js
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* mainMeshNetFunctions.js ( Brainchop main functions)
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* mainNiftiReadingFunctions.js (Nifti functions)
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* mainParameters.js
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* python
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* MRI (data)
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* ExperimentalMode
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* ModelToLoad (Models)
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* model11_gw_ae
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* colorLUT.json (Seg ROI Color Data)
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* labels.json (Seg ROI Labels)
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* group1-shard1of1.bin (Model Weights Binary file)
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* model.json (Model JSON file)
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* css
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* features
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* boundaries
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## How Can I Contribute?
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Include details about your configuration and environment:
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* **Which version of OS, Browser, GPU, CPU you are using**?
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* **Which version of OS, Browser, GPU, CPU are you using**?
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* **What size of RAM you are using**?
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* **Which model you used with the problem**?
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Please follow these steps to have your contribution considered by the maintainers:
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1. Fork Brainchop repository to have a copy on your github.
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2. Push your updates to the forked Brainchop repository on your github.
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3. Into your forked Brainchop repository create a pull request, it should show you the base repository (original one) and the head repository (forked one), choose master branch for each and create pull request
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1. Fork HistoJS repository to have a copy on your github.
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2. Push your updates to the forked HistoJS repository on your github.
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3. Into your forked HistoJS repository create a pull request, it should show you the base repository (original one) and the head repository (forked one), choose master branch for each and create pull request
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4. After you submit your pull request, verify that all [status checks](https://help.github.com/articles/about-status-checks/) are passing <details><summary>What if the status checks are failing?</summary>If a status check is failing, and you believe that the failure is unrelated to your change, please leave a comment on the pull request explaining why you believe the failure is unrelated. A maintainer will re-run the status check for you. If we conclude that the failure was a false positive, then we will open an issue to track that problem with our status check suite.</details>
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5. Don't delete your forked repository until your pull request approved and merged.

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