Setting up Python API

[tattard]

Hi,

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.

Thanks,
Thomas Attard

[manics]

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).