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).
Table of Contents
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. Because PyReconstruct uses your operating system's theme in most cases, its appearance will differ between computers.
Field
The current section's image is displayed in the "field", which appears as a black background in PyReconstruct.
Tools
| Tools | Description |
|---|---|
| Pointer. This tool does blah blah blah... Right clicking on it does blah blah blah... |
| Pan/Zoom. This tool blah blah blah. |
| Scalpel. This tool... |
| Scissors. Blah blah... |
| Closed trace. Blah blah... |
| Open trace. Blah blah... |
| Stamp. Blah blah... |
| Grid. Blah blah... |
| Flag. Blah blah... |
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...