This page serves and its subpages serve 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
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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
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Open trace. Blah blah...
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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..You can navigate around this wiki by clicking the links below or in the sidebar to the left.
| Install PyReconstruct and get it up and running. | |
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| Go all out and get the developer version of PyReconstruct. | |
| Start a new series and begin tracing. | |
| Understand the layout and the various functions of the main window. | |
| Find out more about alignments and aligning. | |
| Get access to lists and list operations. | |
| Learn how to filter using regular expressions. | |
| Perform operations with and to your series. | |
| Visualize objects in three dimensions. | |
| Make sure your work is in tip-top shape. | |
| Leave comments in the field, assign curators to objects, and more. | |
| Explore a random collection of possibilities. |