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Biology](https://img.shields.io/badge/CommsBio-10.1038/s42003--023--05098--1-blue?style=flat)](https://www.nature.com/articles/s42003-023-05098-1)\n[![arXiv](https://img.shields.io/badge/arXiv-2301.04460-b31b1b.svg?style=flat)](https://arxiv.org/abs/2301.04460)\n\nThis repository contains the implementation of [Fast detection of slender bodies in high density microscopy data](https://www.nature.com/articles/s42003-023-05098-1) paper.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/kirkegaardlab/deeptanglelabel/blob/main/docs/figures/tracking.gif\" height=\"236\" /\u003e\n  \u003cimg src=\"https://github.com/kirkegaardlab/deeptanglelabel/blob/main/docs/figures/following.gif\" height=\"236\" /\u003e\n  \u003cimg src=\"https://github.com/kirkegaardlab/deeptanglelabel/blob/main/docs/figures/dense.png\" width=\"720\" /\u003e\n\u003c/p\u003e\n\n## Installation\nTo run the code one must first install the dependencies.\nYou can do this in a virtual environment:\n\n```setup\npython3 -m venv venv\nsource venv/bin/activate\n```\n\nStart by installing `jax` following instructions at their [repository](https://github.com/google/jax?tab=readme-ov-file#installation).\nInstall the remaining dependencies afterwards:\n\n```setup\npip install -r requirements.txt\n```\n\nIf you need to use the model and the auxiliary functions outside this repository, you can install it from the root folder by\n```install\npip install -e .\n```\n\n## Train\nTo train the model, there is a train script used for the model presented in the paper.\nThe possible arguments can be seen by using the help flag.\n```train\npython3 train.py --help\n```\n\nAn example of a training run would be\n```train\npython3 train.py --batch_size=32 --eval_interval=10 --nworms=100,200 --save\n```\n\n## Usage\nExample scripts such as detection and tracking can be found in the [examples folder](./examples)\n\nWe include a Dockerfile (cpu only). For linux we provide a script to run the relevant commands:\n```\n(sudo) sh docker_run.sh\n```\n\n\n## Weights\nThe weights used in the paper can be downloaded from [here](https://sid.erda.dk/share_redirect/cEjIpG1yQl)\nor by using the following commmand\n```download\nwget https://sid.erda.dk/share_redirect/cEjIpG1yQl -O weights.zip\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkirkegaardlab%2Fdeeptangle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkirkegaardlab%2Fdeeptangle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkirkegaardlab%2Fdeeptangle/lists"}