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Top 10 Things to Learn in PyReconstruct

NEU466G, Dr. Harris · Class documents

Overview

These are the ten things to practice first in PyReconstruct. Each one links to more detail in the PyReconstruct Guide. If you have not installed PyReconstruct or opened your series yet, start with Getting started.

Before you start, set your username: go to File > Change username..., type your UT EID, and click OK. You only need to do this once.

1. Open a series

  1. Press Ctrl+O (Mac: Cmd+O), or go to File > Open series....
  2. Select your .jser file and open it.

2. Pan and zoom

  1. In the Tools window, click Pan/Zoom.
  2. Hold down the left button and move the mouse to move the image.
  3. Hold down the right button and move the mouse toward or away from you to zoom in and out.
The Pan/Zoom tool icon
Pan/Zoom.

3. Go between sections

Each image is called a section, and all the sections together form a series. Use the mouse scroll wheel, or Page Up and Page Down, to go up or down through the sections. The status bar at the bottom left shows which section you are on.

4. Rename a trace palette square

  1. Right-click a square in the trace palette. The Set Attributes dialog opens.
  2. In Name, type practicetrace.
  3. Click OK.

Use practicetrace to practice your tracing.

The Set Attributes dialog for practicetrace
Set Attributes for the "practicetrace" square.

5. Draw traces

  • Open or closed: the Open Trace tool draws lines; the Closed Trace tool draws closed loops.
  • Drag or point by point: hold down the left button and move the mouse to draw, or click once and keep clicking to draw point by point. Right-click to finish a point-by-point trace.
The Closed Trace and Open Trace tool icons
Closed Trace (top) and Open Trace (bottom).

6. Merge 2 traces

If 2 closed traces have the same name, overlap, and are both selected, press Shift+M to merge them into one trace.

Two overlapping green closed traces named practicetrace over a round profile, both selected, before merging One green closed trace around the same round profile, after merging
Two overlapping traces with the same name (left) become one trace after Shift+M (right).

Clip: two overlapping green practicetrace loops over a round profile; the pointer clicks the first loop, then the second, so both are selected; Shift+M merges them into one outline.

▶ 8 s · loops

Click one trace, click the other, then press Shift+M.

7. Trace something

  1. Click your practicetrace palette square.
  2. Click the Closed Trace tool.
  3. Choose a small object and trace its outline.
  4. Go to the next section (Page Up) and trace the same object again.
  5. Do this on 3 sections in a row.

Clip: the pointer clicks the Closed Trace tool, holds the left button and drags around a spine head on section 70, and lets go; the new red practicetrace trace is selected.

▶ 13 s · loops

Hold the left button, drag around the object, and let go.

8. Open the Object List

Go to Lists > Object list (Ctrl+Shift+O; Mac: Cmd+Shift+O).

9. View your object in 3D

In the Object List, right-click practicetrace and choose 3D > Add to scene.

Clip: in the Object List the pointer clicks d03, right-clicks it and chooses 3D > Add to scene; the 3D window opens with the dendrite d03, and a drag across the window turns it.

▶ 18 s · loops

Right-click > 3D > Add to scene, then drag in the 3D window to turn the view.

10. Save

Press Ctrl+S (Mac: Cmd+S). Save often while you work.