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Setting up Python API

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Setting up Python API

Postby tattard » Wed May 01, 2019 2:34 pm


I would like to set up a Python (and R) API in a Jupyter Notebook using images from our server directly by connecting via BlitzGateway. As discussed in the Dundee workshop, I am not able to connect to our host server as they were 'locked' onto the Dundee training servers (from what I can remember).

Is there a way to resolve this? I am just trying to analyse some of the images on our server in a similar manner as the FRAP analysis examples in the workshop.

Any help you may provide would be greatly appreciated.

Thomas Attard
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Joined: Wed May 01, 2019 10:42 am

Re: Setting up Python API

Postby manics » Fri May 03, 2019 9:49 am

Hi Thomas

The easiest way to repeat the training workflow on your own system is to install Docker. You can install Docker for Windows or Mac here: https://hub.docker.com/?overlay=onboarding
If you're on Linux Docker may be available in your distribution repositories.

You can then run
Code: Select all
docker run -it -p 8888:8888 openmicroscopy/training-notebooks:0.4.1 jupyter-lab

on the command line to start up the Jupyter server, which you can access at http://localhost:8888/ (the full URL will be printed out when Jupyter starts).
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