This page serves as a preliminary user guide for PyReconstruct, an extensible successor to RECONSTRUCT™ written from the ground up in Python. Please have a look at the source code on our lab's GitHub site. Question can be directed toward PyReconstruct's primary developers, Julian Falco (julian.falco@utexas.edu) and Michael Chirillo (m.chirillo@utexas.edu).

Basics

Installation
   - Launching
   - Starting new series

Images

   - Change img dir
   - Convert to zarr

Main window 

The main window is the first window to open when PyReconstruct is launched. Most of your time working with PyReconstruct will be spent in this window. The current section's image is displayed in the "field", which appears as a black background in PyReconstruct.

Field

<This is all about field...>

Tools

<One-by-one>

Palette

Editing trace-palette
Multiple trace palettes
Increment buttons

Visibility / viewing

<Visibility of viewing>

List / List-operations

   - Regular expressions
   - Section lists / operations
   - Trace list / tags
   - Object list / groups
   - Z-trace list

3D scene

3D Scene stuff...

Series operations

Calibration
Alignments (importing, changing, etc.)
Propagation operations
Importing / exporting
      - Importing traces (no duplicates imported)
      - Importing alignments
      - Importing palettes
      - Exporting back to legacy (remember some data lost)

Meta-data

Commenting / Flags

Curating

Miscellaneous

Extra stuff here...