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nickelnine37 / immue-cell-migration-models

This is a repository for holding prototypes and work in progress for my MSc dissertation on inferring model parameters to describe leukocyte migration.
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immue-cell-migration-models

This is a repository holding the code relevant for my masters dissertation at Edinburgh University entitled "A Cell-Tracking Tool for Analysing Cell Behaviour During Wound Repair". The purpose is to use in-vivo images of white blood cells migrating towards a wound in the wing of a fruit fly, and to build a model for this motion with the aim of inferring infomation about the chemical environment.

Instructions for running with docker

To explore this project via the code in the notebooks folder run the following: 

git clone https://github.com/nickelnine37/immue-cell-migration-models.git
cd immue-cell-migration-models
docker build -t diss .
docker run -p 8888:8888 diss

This may take around 5 minutes and use up ~1.5GB of space. To reduce space and increase build time, remove the following line in the dockerfile

RUN apt update && apt install -y ffmpeg

This will remove the ability to create mp4 videos in notebook 4, but all other functionality will remain.