DOCS: Tutorial on how to run a pipeline
Summary
Tutorial on how to run a pipeline to segment an experiment.
Current behaviour/setbacks
This tutorial does not currently exist in the main documentation; therefore, users don't have an easy entry point into using aliby.
Desired behaviour/advantages
Have instruction on how to run a segmentation pipeline.
New instructions should replace the current 'quickstart documentation' which addresses setting up an Omero sever, data access, tiling, etc. -- these tasks are more advanced and could be moved to elsewhere in the documentation.
Implementation sketch
-
Write documentation in docs/
and include code based on therun.py
code. -
Add docstrings to explain general parameters in the PipelineParameters
object, so that they are included in the Sphix documentation. Then create a link on the run-pipeline page that refers to the page that explains the general parameters.