Feature Suggestion: Interactive CNMF Debug Stage Viewer with Napari

[shirgalor]

I've developed an interactive visualization tool for debugging and analyzing CNMF pipeline stages using Napari. This tool allows users to inspect intermediate results at each stage of the CNMF algorithm (initialization, spatial updates, temporal updates, merging, and refinement), making it easier to understand component evolution and diagnose issues.

Motivation
When running CNMF analysis, it's often difficult to understand:

Why certain components are detected or missed
How components change through spatial/temporal updates
The effect of merging on final results
Whether the algorithm is behaving as expected
This tool addresses these challenges by providing real-time visualization and analysis of each pipeline stage.

Features

-Stage Switching: Navigate between all CNMF debug stages using keyboard shortcuts
-Interactive ROI Analysis: Click on any ROI to see:
Spatial component visualization
Temporal trace plots
A×C reconstruction
Correlation analysis (CNMF vs raw data)
Quality metrics (SNR, compactness, etc.)
Activity distribution histograms
-Reference Layers: Toggle validation layers including:
Original mean image
Max projection
Reconstructed mean (A×C)
Component density map
Local correlation map
Debug Tracking Integration: Works with a debug_tracker module that saves intermediate CNMF results at each pipeline stage.

Related Changes
This feature also requires adding debug hooks to cnmf.py to save intermediate results at each stage using a debug_tracker module. I can provide these changes as well if there's interest.

Questions for Maintainers
Would this be useful as part of the main CaImAn package or as a separate companion tool?
Are there specific stages or metrics you'd like to see added?

[pgunn]

Hi,
It probably would be best maintained as a separate companion tool (for reasons of dependencies and other things); a few other people have done these things in the past, and we've linked to them in the readme; I'd be happy to link to your tool. You'd also be able to get more credit and if you like extend it to work with other tools down the road if that's the way you want to go.

The keyboard shortcuts for speed thing sounds like a nice design feature; if someone gets a lot of comfort with your tool they could do things pretty quickly.

I'd love to take a look at it if you can send me a link.