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Mmasoud1 committed May 18, 2024
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12 changes: 6 additions & 6 deletions README.md
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# Brainchop [![Version](https://img.shields.io/badge/Version-2.1.0-brightgreen)]() [![JS ](https://img.shields.io/badge/Types-JavaScript-blue)]() [![MIT-License ](https://img.shields.io/badge/license-MIT-green)](https://github.com/neuroneural/brainchop/blob/master/LICENSE) [![tfjs](https://img.shields.io/badge/tfjs-Pre--trained%20Model-blue)](https://github.com/neuroneural/brainchop/tree/master/models/mnm_tfjs_me_test) [![DOI](https://joss.theoj.org/papers/10.21105/joss.05098/status.svg)](https://doi.org/10.21105/joss.05098)
# Brainchop [![Version](https://img.shields.io/badge/Version-4.0.0-brightgreen)]() [![JS ](https://img.shields.io/badge/Types-JavaScript-blue)]() [![MIT-License ](https://img.shields.io/badge/license-MIT-green)](https://github.com/neuroneural/brainchop/blob/master/LICENSE) [![tfjs](https://img.shields.io/badge/tfjs-Pre--trained%20Model-blue)](https://github.com/neuroneural/brainchop/tree/master/models/mnm_tfjs_me_test) [![DOI](https://joss.theoj.org/papers/10.21105/joss.05098/status.svg)](https://doi.org/10.21105/joss.05098)


<div align="center">
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## Live Demo

To see Brainchop in action please click [here](https://neuroneural.github.io/brainchop).
To see Brainchop **v4** in action please click [here](https://neuroneural.github.io/brainchop).


<br>
Expand All @@ -69,7 +69,7 @@ To see Brainchop in action please click [here](https://neuroneural.github.io/br

<img src="https://github.com/neuroneural/brainchop/blob/master/css/images/Brainchop_Niivue.png" width="100%">

**Brainchop v4.0.0 with <a href= "https://github.com/niivue/niivue" target="_blank" style="text-decoration: none"> NiiVue</a> viewer**
**Brainchop <a href= "https://neuroneural.github.io/brainchop/" target="_blank" style="text-decoration: none"> v4 </a> with <a href= "https://github.com/niivue/niivue" target="_blank" style="text-decoration: none"> NiiVue</a> viewer**
</div>

<br>
Expand All @@ -78,7 +78,7 @@ To see Brainchop in action please click [here](https://neuroneural.github.io/br

<img src="https://github.com/neuroneural/brainchop/blob/master/css/images/BrainchopMoreRobustModels.gif" width="60%">

**Brainchop v3.0.0 with more robust models**
**Brainchop <a href= "https://neuroneural.github.io/brainchop/v3" target="_blank" style="text-decoration: none"> v3 </a> with more robust models**
</div>

<br>
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![Interface](https://github.com/neuroneural/brainchop/blob/master/css/images/Input3DEnhancements.gif)

**Brainchop v1.4.0 - v3.4.0 rendering MRI Nifti file in 3D**
**Brainchop <a href= "https://neuroneural.github.io/brainchop/v3" target="_blank" style="text-decoration: none"> v1.4.0 - v3.4.0 </a> rendering MRI Nifti file in 3D**
</div>

<br>
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![Interface](https://github.com/neuroneural/brainchop/blob/master/css/images/Brainchop3D.gif)


**Brainchop v1.3.0 - v3.4.0 rendering segmentation output in 3D**
**Brainchop <a href= "https://neuroneural.github.io/brainchop/v3" target="_blank" style="text-decoration: none"> v1.3.0 - v3.4.0 </a> rendering segmentation output in 3D**
</div>


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**Frontend For Neuroimaging. Open Source**

**[Demo](https://neuroneural.github.io/brainchop) &emsp; [Updates](#Updates) &emsp; [Doc](https://github.com/neuroneural/brainchop/wiki/) &emsp; [News!](#News) &emsp; [Cite](#Citation)**
**[Demo](https://neuroneural.github.io/brainchop/v3) &emsp; [Updates](#Updates) &emsp; [Doc](https://github.com/neuroneural/brainchop/wiki/) &emsp; [News!](#News) &emsp; [Cite](#Citation)**

</div>

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<img src="./css/logo/brainchop_logo.png" width="25%" align="right">

<p align="justify">
<b><a href="https://neuroneural.github.io/brainchop/" style="text-decoration: none"> Brainchop</a></b> brings automatic 3D MRI volumetric segmentation capability to neuroimaging by running a lightweight deep learning model (e.g., <a href="https://medium.com/pytorch/catalyst-neuro-a-3d-brain-segmentation-pipeline-for-mri-b1bb1109276a" target="_blank" style="text-decoration: none"> MeshNet</a>) in the web-browser for inference on the user side.
<b><a href="https://neuroneural.github.io/brainchop/v3" style="text-decoration: none"> Brainchop v3</a></b> brings automatic 3D MRI volumetric segmentation capability to neuroimaging by running a lightweight deep learning model (e.g., <a href="https://medium.com/pytorch/catalyst-neuro-a-3d-brain-segmentation-pipeline-for-mri-b1bb1109276a" target="_blank" style="text-decoration: none"> MeshNet</a>) in the web-browser for inference on the user side.
</p>

<p align="justify">
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<div align="center">

![Interface](https://github.com/neuroneural/brainchop/blob/master/css/images/brainchop_Arch.png)
![Interface](./css/images/brainchop_Arch.png)

**Brainchop high-level architecture**
</div>


<div align="center">

![Interface](https://github.com/neuroneural/brainchop/blob/master/css/images/DL_Arch.png)
![Interface](./css/images/DL_Arch.png)

**MeshNet deep learning architecture used for inference with Brainchop** (MeshNet <a href="https://arxiv.org/pdf/1612.00940.pdf" target="_blank" style="text-decoration: none"> paper</a>)
</div>
Expand All @@ -56,15 +56,15 @@ This basic example provides an overview of the training pipeline for the MeshNet

## Live Demo

To see Brainchop in action please click [here](https://neuroneural.github.io/brainchop).
To see Brainchop v3.4.0 in action please click [here](https://neuroneural.github.io/brainchop/v3).

<br>

## Updates

<div align="center">

<img src="https://github.com/neuroneural/brainchop/blob/master/css/images/BrainchopMoreRobustModels.gif" width="60%">
<img src="./css/images/BrainchopMoreRobustModels.gif" width="60%">

**Brainchop v3.0.0 with more robust models**
</div>
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<div align="center">

![Interface](https://github.com/neuroneural/brainchop/blob/master/css/images/Input3DEnhancements.gif)
![Interface](./css/images/Input3DEnhancements.gif)

**Brainchop v1.4.0 rendering MRI Nifti file in 3D**
</div>
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<div align="center">

![Interface](https://github.com/neuroneural/brainchop/blob/master/css/images/Brainchop3D.gif)
![Interface](./css/images/Brainchop3D.gif)


**Brainchop v1.3.0 rendering segmentation output in 3D**
Expand All @@ -98,7 +98,7 @@ To see Brainchop in action please click [here](https://neuroneural.github.io/br
* Brainchop [v2.2.0](https://github.com/neuroneural/brainchop/releases/tag/v2.2.0) paper is accepted in the 21st IEEE International Symposium on Biomedical Imaging ([ISBI 2024](https://biomedicalimaging.org/2024/)). Lengthy arXiv version can be found [here](https://arxiv.org/abs/2310.16162).

<div align="center">
<img src="https://github.com/neuroneural/brainchop/blob/master/css/news/ISBI_2024.jpeg" width="40%">
<img src="./css/news/ISBI_2024.jpeg" width="40%">
</div>

<br>
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* Brainchop [paper](https://doi.org/10.21105/joss.05098) is published in the Journal of Open Source Software (JOSS) on March 28, 2023.

<div align="center">
<a href="https://doi.org/10.21105/joss.05098"><img src="https://github.com/neuroneural/brainchop/blob/master/css/news/JOSS_Logo.png"></a>
<a href="https://doi.org/10.21105/joss.05098"><img src="./css/news/JOSS_Logo.png"></a>
</div>

<br>
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* Brainchop abstract is accepted for poster presentation during the 2023 [OHBM](https://www.humanbrainmapping.org/) Annual Meeting.

<div align="center">
<img src="https://github.com/neuroneural/brainchop/blob/master/css/news/OHBM_2023.jpeg" width="40%">
<img src="./css/news/OHBM_2023.jpeg" width="40%">
</div>

<br>
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* Brainchop 1-page abstract and poster is accepted in 20th IEEE International Symposium on Biomedical Imaging ([ISBI 2023](https://2023.biomedicalimaging.org/en/))

<div align="center">
<img src="https://github.com/neuroneural/brainchop/blob/master/css/news/ISBI_2023.png" width="40%">
<img src="./css/news/ISBI_2023.png" width="40%">
</div>

<br>
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* Google, Tensorflow community spotlight award for brainchop (Sept 2022) on [Linkedin](https://www.linkedin.com/posts/tensorflow-community_github-neuroneuralbrainchop-brainchop-activity-6978796859532181504-cfCW?utm_source=share&utm_medium=member_desktop) and [Twitter](https://twitter.com/TensorFlow/status/1572980019999264774)

<div align="center">
<img src="https://github.com/neuroneural/brainchop/blob/master/css/news/TF_CommunityAward.png" width="60%">
<img src="./css/news/TF_CommunityAward.png" width="60%">
</div>

<br>
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* Brainchop invited to [Pytorch](https://pytorch.org/ecosystem/ptc/2022) flag conference, New Orleans, Louisiana (Dec 2022)

<div align="center">
<img src="https://github.com/neuroneural/brainchop/blob/master/css/news/Pytorch_Poster.jpg" width="50%">
<img src="./css/news/Pytorch_Poster.jpg" width="50%">
</div>


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* Brainchop invited to TensorFlow.js Show & Tell episode #7 (Jul 2022).

<div align="center">
<img src="https://github.com/neuroneural/brainchop/blob/master/css/news/TF_show_tell.png" width="50%">
<img src="./css/news/TF_show_tell.png" width="50%">
</div>

## Citation
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<br />
<div align="center">

<img src='https://github.com/neuroneural/brainchop/blob/master/css/logo/TReNDS_logo.jpg' width='300' height='100'></img>
<img src='./css/logo/TReNDS_logo.jpg' width='300' height='100'></img>

**Mohamed Masoud - Sergey Plis - 2024**
</div>
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# Brainchop [![Version](https://img.shields.io/badge/Version-3.4.0-brightgreen)]() [![JS ](https://img.shields.io/badge/Types-JavaScript-blue)]() [![MIT-License ](https://img.shields.io/badge/license-MIT-green)](https://github.com/neuroneural/brainchop/blob/master/LICENSE) [![Pass ](https://img.shields.io/badge/Pass-OK-green)](https://neuroneural.github.io/brainchop/test/runner.html)
# Brainchop [![Version](https://img.shields.io/badge/Version-3.4.0-brightgreen)]() [![JS ](https://img.shields.io/badge/Types-JavaScript-blue)]() [![MIT-License ](https://img.shields.io/badge/license-MIT-green)](https://github.com/neuroneural/brainchop/blob/master/LICENSE) [![Pass ](https://img.shields.io/badge/Pass-OK-green)](./runner.html)




## Unit Testing

**Mocha** unit testing is available in the browser with this [link](https://neuroneural.github.io/brainchop/v3/test/runner.html).
**Mocha** unit testing is available in the browser with this [link](./runner.html).


<br />
<br />
<div align="center">

<img src='https://github.com/neuroneural/brainchop/blob/master/css/logo/TReNDS_logo.jpg' width='300' height='100'></img>
<img src='../css/logo/TReNDS_logo.jpg' width='300' height='100'></img>

**Mohamed Masoud - Sergey Plis - 2024**
</div>

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