CShaper

<p align="center"><img alt="Logo" src="./assets/logo.png"></p> <br> <p align="justify">This is the official implementation of <a href="https://www.nature.com/articles/s41467-020-19863-x">CShaper</a> published by <I>Nature Communications</I>. It is developed for segmenting densely distributed cells at single-cell elevel, supporting detailed morphological analysis on developmental cells with live-cell microscopy. CShaper was extensively tested on <i>C. elegans</i>, but it should work for other kinds of membrane images (possibly with re-retraining process).</p> <h2>Usage</h2> <p align="justify"><b>Note</b>: This repository targets for runing CShapper with command lines. If you want to process your data with user-friendly GUI, pls prefer to <a href="https://github.com/cao13jf/CShaperApp" target="_blank">CShaperApp</a>.</p> <p align="justify"><b>Step 1</b>: clone this repository and install requirements with conda:</p> <pre><code class="language-bash"> git clone --depth 1 https://github.com/cao13jf/CShaper.git cd CShaper conda env create -f environment.yml </code></pre> <p align="justify"><b>Step 2</b> (optional): train CShaper. Parameters in <code>configs/train.txt</code> should be adjusted accordingly. You may refer to the <a href="https://portland-my.sharepoint.com/:f:/g/personal/jfcao3-c_my_cityu_edu_hk/Es_8Yqeb2jVMvbwGeXxM8gYBE62PmkotlyfxazI9LpI0Dw?e=1HogRY">example data</a> to organize your own dataset.</p> <pre><code class="language-bash"> python train.py --cf configs/train.txt </code></pre> <p align="justify"><b>Step 3</b>: Test CShaper. Parameters for testing CShaper are listed in <code>configs/test.txt</code>. Pretrained model can be downloaded at <a href="https://drive.google.com/drive/folders/1qJ9vJZaXENqiw0x9SGDuFiXTgmkfovVd?usp=drive_link">Google Drive</a>.</p> <pre><code class="language-bash"> python test.py --cf configs/test.txt </code></pre> <p align="justify"><b>Note</b>: Code for shape analysis is not included in this repository.</p> <h2>Correspondence</h2> <p>Please contact Jianfeng Cao at jianfeng13.cao(at)gmail.com if you have any question about the source code or dataset.</p> <h2>Citation</h2> <p align="justify">If this work is useful for you, pls consider the citation.</p> <pre><code> @article{cao2020establishment, title={Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation}, author={Cao, Jianfeng and Guan, Guoye and Ho, Vincy Wing Sze and Wong, Ming-Kin and Chan, Lu-Yan and Tang, Chao and Zhao, Zhongying and Yan, Hong}, journal={Nature communications}, volume={11}, number={1}, pages={6254}, year={2020}, publisher={Nature Publishing Group UK London} } </code></pre>