Quickstart

This page walks through the most common workflow: opening image stacks, tracing a neuron across time, and saving your work.

1. Launch

After installation, start pyDynamo from the command line:

pydynamo_brain

Or open an existing project directly:

pydynamo_brain path/to/my/file.dyn.gz

Two windows will appear: a logo/control window (keep this open until you’re done) and the project window.

2. Start a new project

From the project window, choose New from Stacks (Ctrl-N) and select one or more .tif image files. Each file is a single timepoint volume.

To reopen an existing project, use Open from File (Ctrl-O) and select a .dyn.gz file.

3. Trace the first timepoint

In the stack view:

  1. Click anywhere to place the first point — this should be the soma.

  2. Click into empty space to extend the current branch.

  3. Use the scroll wheel (or keys 1/2) to move through Z-slices.

  4. Right-click (or Ctrl+click) on an existing point to start a new branch from it.

  5. Middle-click (or Shift+click) on an existing point to insert a point mid-branch.

Press Ctrl-S to save. The file will auto-save after the first manual save.

4. Move to the next timepoint

Load the next stack via the stack list. Then either:

  • Press I to import the previous timepoint’s tracing as a starting point.

  • Draw from scratch.

Adjust points to match the new image, then press R on a point to auto-register it and all downstream points to their positions in the new stack.

5. Key shortcuts

Key

Action

1 / 2

Move Z-slice down / up

W A S D

Pan the image

X / Z

Zoom in / out

R

Auto-register selected point and subtree

P

Toggle puncta mode

F

Cycle annotations / IDs / none

T

Tile all visible stacks

F1

Open full help dialog

Ctrl-S

Save

Ctrl-Z

Undo

See the Drawing and Registration pages for more detail.