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CTFishPy

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Automatic segmentation of zebrafish bone from uCT data using deep learning.

Installation

pip install git+https://github.com/wahabk/ctfishpy

Usage

Check the jupyter notebooks in examples/

Dependencies

For python dependencies check setup.py

Dev

Docker

I provide a docker image to make gpu training easier

Step 1 : Build image, this will build an image named zebrafish

docker build . --tag=zebrafish 
docker build . --tag=zebrafish --network=host # if you're on vpn

Step 2 : Create container in interactive mode, this will start a shell inside the container

docker run -it \
	-v <data_dir>:<data_dir> \ # mount data directory as volume
	-v <repo_dir>:/colloidoscope \ # mount git repo directory as volume for interactive access
	--gpus all \ # allow the container to use all gpus
	--network=host \ # if you're on vpn
	zebrafish \ 

Note: If you want to launch the container on a custom hard drive use:

sudo dockerd --data-root <custom_dir>

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Project to analyse fish CT data

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