Reports

mesoscopy report writes a self-contained HTML report for a pipeline output and picks the report from the filename suffix. The report lands next to the input, or under -o.

mesoscopy report /path/to/recording_preprocessed.h5
mesoscopy report /path/to/recording_registered.h5
mesoscopy report /path/to/recording_smoothed_regions_event-cueonset_perievent.csv -o /path/to/reports

Reports need an internet connection to render and are otherwise self-contained.

Preprocessing report

For a *_preprocessed.h5 written by preprocess. It shows the session metadata, the automated QA checks (histogram separation, timestamp consistency and jumps, noise, SNR, bleaching), the timestamp series and its jumps, the per-frame statistics used for channel separation and the resulting frame assignment, the mean ∆F/F of each channel, and the haemodynamics-corrected ∆F/F with its projections and an example frame.

Registration report

For a *_registered.h5 written by register landmarks. It shows the recording landmarks against the template landmarks before and after the affine transform, and a registered frame with the template landmarks overlaid.

Peri-event report

For a *_perievent.csv written by process peri-event. It shows each region's response around the event as the mean ± 95% CI across trials or as individual trials, filtered by trial type, one region at a time and as a grid of every region. Choose the region from the dropdown, by clicking the Allen CCF top view, or by clicking a panel in the grid.

When the *_metrics.csv and *_metrics-session.csv from process metrics sit next to the input, the report adds a metrics section. It marks the onset, peak and offset on the traces with the across-trial spread of each, plots per-trial box plots for the selected region, colours the atlas by a session metric, and lists the session table. The atlas and the session table follow the trial group chosen above the table, and for go/no-go sessions the table also shows the reliability metrics. Peri-event files written without the trials columns have no trial types. Pass the trials CSV with -t/--trials to recover them.

When the *_connectivity.csv from process connectivity sits next to the input, the report adds a connectivity section. It shows the chosen metric for the chosen trial group as a region by region heatmap, and the trial group follows the selector above the session table. The transfer entropy and its z-score are directed, from the row region to the column region. Click a cell to select its row region in the rest of the report.