Cell Profiler - Githubissues

ome / training-notebooks

A set of Python Notebooks to demonstrate how to access the images and metadata from OMERO

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Cell Profiler #11

Closed jburel closed 6 years ago

jburel commented 6 years ago

Install the latest version of CellProfiler (v3.1.3) and fix the notebook

Available at https://ome-lochy.openmicroscopy.org/jupyterhub-training/

To test:

Run the notebook against outreach as trainer-1, Use the dataset "Cell Profiler Image"
Make sure that the R notebook still works

To build and test it locally:

docker build -t training-notebooks .
docker run -it -p 8888:8888 training-notebooks

dominikl commented 6 years ago

The R notebook still works, but the CellProfiler notebook doesn't. Running the first cell gives UnboundLocalError: local variable 'jdk_dir' referenced before assignment .

jburel commented 6 years ago

That is due to the fact that I brought R back ( I removed it at the start) Ok I know what the problem is

dominikl commented 6 years ago

Both notebooks work now. Good to merge 👍

joshmoore commented 6 years ago

Didn't get a chance to play with it yet, but certainly looking forward to it. Merging. (Only thing we may want to do in a follow-up is optimize the image size to speed up pull times)

jburel commented 6 years ago

When we have a better idea of what we need for training and IDR some of it will be moved to jupyter-docker this could be a good opportunity to do that