This document should serve as a collection of links to more detailed documentation, tips or tricks how to use the Python Microscopy Environment or PYME for short.
This is still in some early alpha phase and contains various place holders etc. If you have useful feedback please let us know in this repo's issue tracker.
- link to the latest PYME documentation at python-microscopy.org
- the main PYME website - python-microscopy.org
- installation instructions at python-microscopy.org
- this repository: pyme-install-docs
We like the concept of launchers for windows PYME installs. This allows you to have various Python (or more specifically conda) virtualenvs and fire up PYME apps in these environments seamlessly.
The general concept is described on the PYME windows launchers page.
Some examples can be found in the launchers subfolder of our site-config repository.
A basic overview how to save and load data processing pipelines in PYME.
Video Link (via Panopto, accessible only for UoE staff): PYME - Saving and loading visgui recipes
A basic overview how to find (locate) and then select fiducial information in PYME. This is describing the approach via PYME-extra which implements a version where we select a single fiducial and does not suffer from the problem we see using the general PYME fiducial module approach which in our hands leads to broken segments. This really needs a discussion between David and us to solve this issue properly at some stage!
The downside of our single fiducial approach is that we cannot easily take advantage of averaging.
Video Link (via Panopto, accessible only for UoE staff): PYME - finding and selecting fiducials
A basic overview how to apply fiducial information to drift correct a data series in PYME.
Video Link (via Panopto, accessible only for UoE staff): PYME - applying fiducials for drift correction
This should link to a future quick overview of how this can be done.
- template repository that shows how to make plugin repositories: pyme-plugin
- more stuff?