#+title: PyPhenix workshop
#+subtitle: a workshop for getting started with PyPhenix
#+author: Max Ferrin
#+email: ferrin@calicolabs.com
#+last_modified: <2026-03-10 Tue 15:11>
#+OPTIONS: toc:t num:nil author:t date:t title:t ^:nil broken-links:mark
* Aims
** General
- visualize data with PyPhenix
- explore how PyPhenix can serve as a starting point for downstream processing
  and analysis
- share feedback to improve or extend PyPhenix
** Data preparation
- How to export from Opera Phenix
** Graphical session
- install PyPhenix widget and all dependencies on your computer
- learn the basic functions of the PyPhenix widget:
  - load a dataset
  - select dimensions for visualization
  - show physical pixel size and real time stamp
  - 2D and 3D view
  - thick/thin slicing
  - adjust colormaps and contrast limits
  - simple napari console commands
** Scripting session
- install dependencies necessary to run jupyter notebooks
- learn the basic functions of the PyPhenix scripting functions:
  - launch viewer from interactive notebook
  - print out metadata
  - load a specific subset of data
  - loop through multiple wells
  - carry data forward for python-based processing with numpy arrays 
* Brainstorming
** unorganized
- shout out pyphenix google chat group
** downstream tools
- explore [[https://napari-hub.org/][napari hub]] together
  - keep track of compatibility: plugin engine was recently overhauled
- make movies using [[https://napari.org/napari-animation/][napari-animation]]
- some kind of graphical segmentation helper?
* 
