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Image for working with OME Files in Jupyter
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OME Files Jupyter

Image for working with ome-files-py in Jupyter.

Run as:

docker run --rm -it -p 8888:8888 openmicroscopy/ome-files-jupyter

Copy the URL displayed in the startup log and paste it in your browser. In the dashboard, you should see an example notebook from ome-files-py. Within the container, this is stored in /home/jupyter/notebooks. This means that you can override the default example with your own set of notebooks by mounting the host directory that contains them (e.g. /my/notebooks) as a data volume on top of /home/jupyter/notebooks:

docker run --rm -it -p 8888:8888 -v /my/notebooks:/home/jupyter/notebooks openmicroscopy/ome-files-jupyter

Choosing a kernel

The Jupyter server in the image has both the Python 2 and the Python 3 kernel installed. This means you can use notebooks written in either version. To create a new Python3 notebook, for instance, choose New > Python 3 in the main Jupyter dashboard. To change kernel for an existing notebook, choose Kernel > Change kernel from the notebook GUI.

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