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DataJoint pipeline to capture the data for the mice two-photon imaging experiments in the presence of olfactory stimulation.
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This is a clone of the cajal/pipeline with modifications.
- Launch a new terminal and run the following
cd ~/<Enter custom path> git clone https://github.com/reimerlab/odor_meso git clone --branch release-1.0 https://github.com/ppfaff/DataPlot cd odor_meso
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At the root of the
odor_mesorepository folder, create a new file.envfrom theenv_template. -
Specify the database's
DJ_HOST,DJ_USER, andDJ_PASS.
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This file is required for the
DataManandplot_dmfunctions. -
At the root of the
odor_mesorepository folder, create apaths.initfile and auinit.initfile.
- Under
ports: HOST:CONTAINER, if theHOSTport is in use you will need to change this port.
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Install Docker Desktop
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From the root of the cloned
odor_mesorepository directorydocker-compose up -d --build notebook
- At this point the basic setup of this pipeline is complete.
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The following is a resource for docker commands you may need to utilize.
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Build the Docker image
docker-compose up -d --build notebook -
If the image is already built, start a container
docker-compose up -d notebook -
Access an interactive bash shell of the container
docker exec -it odor_meso_notebook_1 /bin/bash -
Stop and remove containers and networks
docker-compose down
- The data ingestion and processing is usually handled with an automatic procedure, but the steps are described within the following Jupyter Notebook. To run the notebook, navigate to
localhost:8888in your web broswer.~/odor_meso/python/scripts/data_ingest.ipynb
- Detailed instructions can be found within the following Jupyter Notebook. To run the notebook, navigate to
localhost:8888in your web broswer.~/odor_meso/python/scripts/data_explore.ipynb