GUI guide

This section walks through the napari app one panel at a time. Start with What you see on launch, then jump to the task you need.

Tasks

• Loading recordings
• Drawing and generating ROIs
• Response plots and heatmaps
• Running custom workflows
• Matching cells across recordings
• Saving and exporting

What you see on launch

Run twopy (optionally with a recording path) and napari opens with four docks around the viewer:

• Top — twopy responses: response trace plots and a Heatmaps tab. Reads from the current ROIs and processing settings.

• Right — twopy: the tabbed control sidebar. Tabs in order: Load, Metadata, Plot, ROIs, Epochs, Custom, Export.

• Center — viewer layers: mean image, optional aligned movie, and an editable rois Labels layer.

• Bottom — twopy trial timeline: shows stimulus epochs across the recording. Click or drag the rail to seek the movie; gray / interleave epochs render as neutral gray. The viewer HUD reports the current trial and epoch.

If no recording is loaded yet, the docks still appear. Pick one from the Load tab to populate them.

Where each task lives

I want to…	Tab or window
Find and open recordings	Load tab
Look at acquisition info and save paths	Metadata tab
Draw ROIs or generate them automatically	ROIs tab
Change response window, dF/F, smoothing, heatmaps	Plot tab
Hide stimulus epochs from plots	Epochs tab
Run Direction selectivity or your own workflow	Custom tab
Match the same cell across recordings	Open Group Matching button
Save analysis or export figures	Export tab

The two-photon timing contract

Imaging and stimulus presentation run on separate computers. The photodiode signal in the recording is the bridge: twopy uses it to align stimulus events to imaging frames. You can ignore this when using the app — twopy aligns the timing for you — but it explains why ROI responses use photodiode-aligned epoch windows rather than nominal frame rates. See Input data spec for the contract.