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PyReconstruct User Guide

PyReconstruct is a desktop application for tracing, annotating, and 3D-reconstructing serial-section and volume electron-microscopy (EM) data. This guide covers installing the app, opening and building a series, the tracing tools, the data lists, alignment, 3D reconstruction, and backups.

This guide describes the application as it currently behaves in this distribution. It complements the in-app help (Help ▸ Online resources ▸ PyReconstruct user guide, which opens the lab wiki at The University of Texas at Austin) and the in-app Help ▸ Shortcuts list.

About screenshots. This guide does not ship screenshots yet. Places where a screenshot would help are marked like this:

📸 Screenshot: short description of what to capture.

Contributions of screenshots are welcome — see CONTRIBUTING.md.

Shortcuts. Key combinations shown here are the defaults. Almost all of them are rebindable under Help ▸ Shortcuts list (press ?). A few menu shortcuts are fixed: PgUp/PgDown (section navigation), Home (fit view), Ctrl+\ (align by correlation), and ? (the shortcuts list itself).

Contents

Getting started

• Installing PyReconstruct
• Keeping PyReconstruct Up to Date

Concepts

• Core Concepts

Using PyReconstruct

• Opening and Creating a Series
• The Main Window and Navigation
• The Tool Palette
• The Trace Palette
• Working with Traces
• Data Lists
• Alignment
• 3D Reconstruction
• Saving and Backups

Reference

• Keyboard Shortcuts
• Getting Help
• Credits