Datasets:

eulerlab
/

eyewire2-data

Loaded via data_loader.load_df_rois() (concatenates all 5 files and adds qfilt). One row per ROI (cell). 380 rows x 84 columns across the 5 files combined.

General / recording metadata

experimenter: Name of the experimenter who conducted the recording.
date: Date of the experiment.
exp_num: Experiment number for the given date. Typically corresponds to the eye: 1 = left eye, 2 = right eye.
raw_id: Internal recording/table index from the acquisition pipeline; not meaningful for analysis on its own.
field: Field identifier in the experiment ("GCL" + a number indicating the sequential order of the field within the recording session).
region: Anatomical region of the recording field. Values seen: "RR" (Right Retina).
cond1, cond2: Experimental condition identifiers for the recording (e.g. "control"); distinguish e.g. drug/control conditions when an experiment has more than one.
ch0_name, ch1_name: Names of the two acquisition channels (e.g. wDataCh0 = OGB-1/calcium indicator channel, wDataCh1 = SR-101/structural astrocyte-marker channel, based on ch0_average/ch1_average usage elsewhere in the codebase).
roi_id: ROI identifier within the field.
chirp, bar: Stimulus identifiers for the chirp (gChirp) and moving-bar (movingbar) stimulus protocols.
preprocess_id, classifier_id: Internal pipeline version/step identifiers (which preprocessing/classifier run produced this row); not meaningful for analysis on their own.
chirp_stim_name, bar_stim_name: Stimulus protocol names, redundant with chirp/bar.
genline: Genetic line of the animal (typically "Bl6").
animgender: Sex of the animal.
eye: Eye used for recording ("left" or "right").
setupid: Identifier of the physical 2P rig/setup used for acquisition.
prepwmorient: Orientation of the eye-cup preparation in degrees. 0 deg indicates dorsal is toward the back of the chamber; -1 indicates unknown orientation.
nxpix, nypix: Width/height of the recorded field in pixels.
pixel_size_um: Physical size of one pixel in micrometers.
field_ventral_dorsal_pos_um, field_temporal_nasal_pos_um: Position of the recording field's center relative to the optic nerve, in micrometers (negative ventral/temporal, positive dorsal/nasal) — same value repeated for all ROIs in a field, see the corresponding columns in df_eyewire2_field_level.parquet.
ch0_average, ch1_average: Average-intensity images (2D, nxpix x nypix) of the two acquisition channels for the ROI's field.

ROI geometry

roi_size_um2: Area of the ROI mask in square micrometers.
roi_dia_um: Circle-equivalent diameter of the ROI mask in micrometers.
ventral_dorsal_pos_um: Ventral-dorsal position of this ROI relative to the optic nerve, in micrometers (negative = ventral, positive = dorsal).
temporal_nasal_pos_um: Temporal-nasal position of this ROI relative to the optic nerve, in micrometers (negative = temporal, positive = nasal).

Chirp stimulus responses

chirp_trace: Raw fluorescence trace during chirp stimulus presentation (1D array, one value per recording sample, all repeats concatenated).
chirp_trace_t0, chirp_trace_dt: Start time and sampling interval (s) of chirp_trace.
chirp_pp_trace: Preprocessed (detrended/normalized) version of chirp_trace.
chirp_pp_trace_t0, chirp_pp_trace_dt: Start time and sampling interval (s) of chirp_pp_trace.
chirp_qidx: Quality index (signal-to-noise ratio) of the chirp response for this ROI.
chirp_pres_qidx: Fraction of ROIs in this ROI's field that pass the chirp quality threshold.
chirp_average_norm: Normalized chirp response, averaged across repeats (1D array).
chirp_average_dt: Sampling interval (s) of chirp_average_norm.
chirp_snippets: Per-repeat chirp response snippets, shape (time_points, n_repeats).
chirp_snippets_t0: Start time of each repeat in chirp_snippets (1D array, one per repeat).
chirp_snippets_dt: Sampling interval (s) of chirp_snippets.
chirp_triggertimes_snippets: Stimulus trigger times per repeat, used to align chirp_snippets (2D array, n_triggers_per_repeat x n_repeats).

Moving-bar stimulus responses

bar_trace: Raw fluorescence trace during moving-bar stimulus presentation (1D array).
bar_trace_t0, bar_trace_dt: Start time and sampling interval (s) of bar_trace.
bar_pp_trace: Preprocessed (detrended/normalized) version of bar_trace.
bar_pp_trace_t0, bar_pp_trace_dt: Start time and sampling interval (s) of bar_pp_trace.
bar_qidx: Quality index for the moving-bar response, calculated using only the preferred direction.
bar_pres_qidx: Fraction of ROIs in this ROI's field that pass the moving-bar quality threshold.
bar_ds_index: Direction-selectivity index (DSi).
bar_ds_pvalue: Statistical p-value for direction selectivity.
bar_pref_dir: Preferred direction in radians.
bar_os_index: Orientation-selectivity index (OSi).
bar_os_pvalue: Statistical p-value for orientation selectivity.
bar_pref_or: Preferred orientation in radians. Not corrected for eye orientation (left vs. right) or experimental setup geometry.
bar_dir_component: Direction-tuning component from a rank-1 SVD decomposition of the direction-sorted moving-bar snippet matrix (one value per stimulus direction, see ds.get_time_dir_kernels).
bar_time_component: Time-kernel component from the same SVD decomposition (one value per time point within a snippet).
bar_snippets: Per-direction moving-bar response snippets, shape (time_points, n_directions).
bar_snippets_t0: Start time of each direction snippet in bar_snippets (1D array).
bar_snippets_dt: Sampling interval (s) of bar_snippets.
bar_triggertimes_snippets: Stimulus trigger times per direction, used to align bar_snippets.

Mouse-cam (natural movie) stimulus responses

mc: Identifier of the mouse-cam movie clip shown (e.g. mc16).
mc_trace: Raw fluorescence trace during mouse-cam movie presentation (1D array).
mc_trace_t0, mc_trace_dt: Start time and sampling interval (s) of mc_trace.
mc_pp_trace: Preprocessed (detrended/normalized) version of mc_trace.
mc_pp_trace_t0, mc_pp_trace_dt: Start time and sampling interval (s) of mc_pp_trace.
mc_triggertimes: Stimulus trigger times marking movie-clip boundaries/repeats during the mouse-cam presentation.

Cell type classification (Baden et al. 2016)

Computed via baden16_utils.baden16_cluster_probs_to_info from probs_per_cluster.

cluster_id: Predicted Baden et al. 2016 functional cluster ID (1-75).
group_id: Predicted Baden et al. 2016 functional group ID (1-46), derived from cluster_id.
supergroup: Predicted broad functional supergroup label (e.g. "OFF", "ON-OFF", "Fast ON", "dAC"), derived from group_id.
prob_cluster: Predicted probability of the assigned cluster_id.
prob_group: Summed probability across all clusters belonging to the assigned group_id.
prob_supergroup: Summed probability across all clusters belonging to the assigned supergroup.
prob_class: Predicted probability of the broad RGC-vs-dAC class implied by supergroup.
probs_per_cluster: Full probability vector (75 values) across all Baden et al. 2016 clusters.

Derived

qfilt: Boolean quality-filter flag, added by data_loader.load_df_rois. True if bar_qidx > 0.6 or chirp_qidx > 0.45.