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

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.

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:

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...