Open Microscopy Environment

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

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).