This page 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). You can navigate around this wiki by clicking the links below or in the sidebar to the left.
List and list operations
Series operations
Meta-data
Miscellaneous
Basics
Installation
- Launching
- Starting new series
Images
- Change img dir
- Convert to zarr
Main window
When PyReconstruct is launched, the window to appear is the main window. Most of your time working with PyReconstruct will be spent in this window. Because PyReconstruct uses your operating system's theme in most cases, the look of the main window might differ slightly between computers. Here is a summary of its various parts:
Field
The current section's image is displayed in the "field", which appears as a black background. The current section, alignment, and x and y position (in microns) of the cursor in the field is displayed in the status bar, which is located in the bottom left of the window.
Tool bar
The tool bar gives you access to the main tools used to work in the field. You can move the tool bar around the field by clicking and holding before moving the tool bar. Select a tool by left-clicking on its icon. In some cases, the tool's options can be changed by right-clicking on the tool's icon.
Here are brief descriptions of each tool:
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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
This stuff about calibration...
Alignments
This stuff about alignments...
Importing / exporting
- Traces
- Aligments
- Palettes
- Exporting back to legacy
Propagation operations
This stuff about propagating
Meta-data
Commenting / Flags
Curating
Miscellaneous
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| 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. |