Typical workflow

Convert recording file to NWB format

mesoscopy convert /path/to/example-recording.h5

Note

See also our guide to converting video files to HDF5 if you're recording videos in AVI or MP4 format.

Inspect raw data

mesoscopy inspect /path/to/example-recording.nwb

Preprocess to correct for haemodynamics and extract ∆F signal

mesoscopy preprocess /path/to/example-recording.nwb

Register to the Allen Brain Atlas

First mark the anatomical landmarks on the recording. This opens the napari landmark GUI, seeded with a point per landmark: drag each one onto its anatomical location, then press Save and Close.

mesoscopy register label /path/to/example-recording.nwb

This writes example-recording_landmarks.csv to the output directory (-o, the current directory by default), holding each landmark's (x, y) position in the pixel space of the ∆F/F series.

Then warp the recording onto the atlas. The landmarks file is found automatically if it sits next to the recording or in the output directory; pass -r/--recording-points to point at it explicitly.

mesoscopy register landmarks /path/to/example-recording.nwb

The registered frames are written in Allen CCF template space at the atlas's own dimensions, which is what mesoscopy process area-responses expects. Use --output-width / --output-height only if you are registering onto a different template.

Note

-t/--template-points supplies the template landmarks being registered onto, not your recording's landmarks. Leave it unset to use the Allen CCF landmarks that ship with mesoscopy.

Registration reports how far each landmark ends up from its template position, and warns if the fit is poor:

Estimating transform from 9 landmarks...
Landmark fit: RMSE 2.28 px, worst is 'rFP' at 3.94 px (in template pixels).

To check the alignment visually, generate the QA report for the registered HDF5 file written by the step above — its path is echoed as Saved registered frames at ...:

mesoscopy report /path/to/example-recording_registered.h5

Extract area responses

mesoscopy process area-responses /path/to/example-recording.nwb