Puncta

Dynamo allows drawing puncta on top of stack images. Puncta are treated as single points with a 3D position and a size (radius). They are useful for marking synapses, boutons, or other discrete structures.

Drawing

Entering puncta mode (P)

Press P to enter and exit puncta mode. While in puncta mode, the bottom of each stack window will show a puncta toolbar.

Selecting puncta

Click on an existing puncta to select it. Selected puncta are highlighted. Puncta can appear in the following states:

  • Normal — unselected puncta at the current Z-slice.

  • Selected — the currently active puncta (shown highlighted).

  • Out-of-plane — puncta from other Z-slices, shown faded if V is enabled.

Adding puncta

Click on empty space to add a new puncta at that X/Y position on the current Z-slice. The puncta will also be propagated forward to later stacks.

Moving puncta

Each puncta has two properties that can be changed:

  • Center position — Shift-click a selected puncta, then click the new position to move it.

  • Radius — use [ and ] to decrease and increase the radius of the selected puncta.

Deleting puncta

Select a puncta by clicking it, then press Delete (or Backspace) to remove it. Deleting a puncta from one stack will remove it from all stacks.

Analysis

Puncta analysis quantifies the presence, size, and change of puncta across timepoints.

Puncta count

The total number of puncta per stack can be viewed in the analysis window (M).

Motility

Puncta that appear, disappear, or move between timepoints are classified as dynamic. This is computed using the same added/subtracted/transitioned framework as branch analysis.

Export

Puncta positions and radii can be exported to CSV via the analysis panel. Each row corresponds to a single puncta instance (stack, X, Y, Z, radius).