Add first version of the idr0021 segmentation notebook

[dominikl]

Adds a notebook which performs the idr0021 segmentation completely in R (to be used for the Cambridge workshop 6th Dec).

Test on : https://ome-lochy.openmicroscopy.org/jupyterhub-internal (training-notebooks:master_merge_daily)

[dominikl]

/cc @pwalczysko @jburel

[pwalczysko]

The idr0021 script here (the one which is FYI only for participants) is working fine -> tried the whole run on user-40, worked as expected.

[pwalczysko]

Finished reading. Several comments, but looks pretty good in general.

[dominikl]

Hope I fixed all your remarks @pwalczysko . Removed the "trainer only" part from the notebook. That was the part which runs the segmentation over the whole idr0021 project in order to generate the trainer-1 'Summary from R' table. Can add that as seperate notebook, if needed. Also added "Task" section in the description of the notebook which outlines each task which is demonstrated by the notebook. But I'm still not sure if it is generic enough to be used as general ITR example notebook, the "Exercise" parts are certainly not.

I still need to add the 'Summary from R' as CSV file to the trainer-1 project, and add another exercise "Download the CSV and open in Excel" at the end of this notebook, but that will be just a small addition.

[dominikl]

From the last testing round I got:

• Use a 'run' flag to en/disable optional exercise block (pixel size exercise)
• Add solution for it to bottom
• Make clear to load the trainer-1 idr0021 project for stats part
• If there's no output, print out at least a message like "Dataframe has been attached".

I'll push another commit addressing these issues later. More feedback welcome. Will try to finalize the notebook until Monday.

[pwalczysko]

Couple of more edits, mainly text improvements.

@dominikl Regarding the scripts for cleanups.

We have scripts which delete:

1. All the ROIs in a specific dataset - this works very well for me https://github.com/ome/training-scripts/blob/master/maintenance/scripts/delete_ROIs.py
2. All annotations (also attachments) on images in a specific dataset https://github.com/ome/training-scripts/blob/master/maintenance/scripts/delete_annotations.py - needs improving, does not iterate through all users

We do not have a script which would delete:

1. All annotations on all specified datasets (not images inside those datasets). This should be probably an additional option of https://github.com/ome/training-scripts/blob/master/maintenance/scripts/delete_annotations.py - that obviously needs improvement

[pwalczysko]

Again, just couple of minor comments, the notebook reads and runs well.

[jburel]

@dominikl Could you fix the minor comments this am? we will need to have that PR merged so we can have the image built and deployed for Monday testing

[dominikl]

Ah sorry, forgot to add/push the changes yesterday. Done now.

[jburel]

Thanks so We will need to trigger the build for a final check

[pwalczysko]

Happy with the changes Ready to merge

[jburel]

Thanks Merging