SLAP2 glutamate QC: Figure 7 panels C/G/K with archive-wide event-based metrics - #171
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SLAP2 glutamate QC: Figure 7 panels C/G/K with archive-wide event-based metrics#171ido4848 wants to merge 3 commits into
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… notebook Event-based signal/noise QC for the SLAP2 glutamate (iGluSnFR4f) sessions of DANDI 001424, mirroring the mesoscope scheme of discussion #156: - slap2_glutamate_qc_events.py: per-session QC library + CLI (matched-filter detection at 3 SD, raw-sigma event amplitudes binned <2 / 2-4 / >4 SD, k-means quality classes, layout-agnostic NWB loading) - slap2_glutamate_qc_batch.py: runs all 20 sessions (8 mice, 2,540 synapses) into per-synapse, per-context and per-session tables; classes fitted per acquisition cohort; per-source context seconds from valid samples - slap2_glutamate_figure7_panels.py: renders panel C (example session) and panels G and K (all sessions) - docs/notebooks/slap2_glutamate_figure7_panels.ipynb + the rendered panels (PNG/SVG) and tables under docs/notebooks/plots_figure7_slap2_glutamate/; notebook added to the mkdocs Analysis nav Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…lasses
Review feedback on the QC figures: "instead of Low SNR / Intermediate / High
SNR, maybe use a colour gradient that maps to the actual SNR values?"
Panels C and G are the two that can carry a colourbar instead of a legend (an
ROI map and a scatter), so `render_panel_c` / `render_panel_g` take an opt-in
`color_by` (`--color-by` on the CLI) and write `*_gradient.{png,svg}` next to
the defaults. Panel K keeps the classes: a stacked or grouped bar needs a
categorical variable, and the three-class scheme is what keeps this column
comparable to the mesoscope column of #156.
Default behaviour is unchanged — re-rendering C/G/K without the flag gives
PNGs byte-identical to the committed ones.
The scalar is `median_event_raw_sd`, the synapse's median event amplitude in
SD of its own noise: same unit as the rest of panel G, and spearman 0.99 with
the > 4 SD fraction the classes are ordered by. `robust_snr` is accepted too
but is a poor gradient — its class medians (2.32 / 2.65 / 2.70 archive-wide)
overlap almost completely and every synapse above 10 is in the glutamate +
calcium cohort, whose non-negative dF/F shrinks sigma.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Adds the SLAP2-glutamate column of Figure 7 (panels C, G, K) together with the event-based QC pipeline behind it, mirroring the mesoscope scheme of #156: events are detected on the matched-filtered ΔF/F at 3 SD of the noise, each event's amplitude is measured on the raw trace in noise SDs and binned < 2 / 2–4 / > 4 SD, and each synapse is classified (k-means, k = 3) by the fractions of its events in the three bins (
slap2_glutamate_qc_events.py).slap2_glutamate_qc_batch.pyruns this over all 20 sessions of DANDI 001424 (8 mice, 2,540 synapses) and the resulting per-synapse, per-context and per-session tables are committed underdocs/notebooks/plots_figure7_slap2_glutamate/, so panels G and K (slap2_glutamate_figure7_panels.py) re-render in seconds without any NWB; only panel C and the example trace in G read one session (sub-794237_ses-20250508T145040, downloaded by the notebook, not committed).Panel C shows both imaging planes of the example session with one synapse's footprint and 20 s of ΔF/F with events; G shows how signal and noise are measured on a trace, the class definition by example, and every synapse of the archive in the event-amplitude feature space; K shows event rate by stimulus context per class and class composition by dendritic compartment and per neuron.
Two choices worth a look: classes are fitted per acquisition cohort (the 12 glutamate-only sessions ship two-sided ΔF/F, the 8 glutamate + calcium sessions non-negative NMF-denoised traces, so one fit over all 20 mostly sorts by pipeline, the tables carry both
quality_classand a per-sessionquality_class_session), and context rates use each source's own recorded seconds because the two DMDs of a session can run for different spans.The walkthrough notebook
docs/notebooks/slap2_glutamate_figure7_panels.ipynb(added to the mkdocs Analysis nav) runs the per-session QC on the example session, loads the archive tables, and renders the panels.