New dataset version, updated stimuli

.gitattributes

@@ -879,3 +879,4 @@ session_Franke_Baden16_2013-04-29/experiment_1_N_A/field_Q1.nwb filter=lfs diff=
 session_Franke_Baden16_2013-04-29/experiment_1_N_A/field_Q3.nwb filter=lfs diff=lfs merge=lfs -text
 session_Franke_Baden16_2013-04-29/experiment_1_N_A/field_Q6.nwb filter=lfs diff=lfs merge=lfs -text
 session_Franke_Baden16_2013-04-29/experiment_1_N_A/field_Q2.nwb filter=lfs diff=lfs merge=lfs -text
+*.nwb filter=lfs diff=lfs merge=lfs -text

FIELDS_DESCRIPTION.md

@@ -0,0 +1,74 @@
+# Field Descriptions for `all_GCL_table.parquet` and `.nwb` files
+
+This document describes the data fields available in the `all_GCL_table.parquet` file and corresponding `.nwb` files.
+
+## General 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
+- **field**: Field identifier in the experiment. Format: "GCL" or "RGC" followed by a number. The number indicates the sequential order of the field within the recording session. Field numbering conventions may vary across experimenters (typically starting at 0 or 1). Some fields may include postfixes (e.g., "a" or "b") to indicate additional experimental conditions or retinal subdivisions
+- **region**: Anatomical region of the recording field. Values: "LR" (Left Retina), "RR" (Right Retina), "RRN" (Right Retina Nasal), "RRT" (Right Retina Temporal)
+- **roi_id**: Region of interest identifier within the field
+- **cond1**: Condition identifier. Values: "C1", "c1", or "control", indicating the first control condition. Some experiments include multiple control or drug conditions
+- **stim_name**: Name of the stimulus protocol used
+- **genline**: Genetic line of the animal (typically "Bl6")
+- **animgender**: Sex of the animal. Values: "female", "male", or "" (empty string indicates missing data)
+- **age**: Age of the animal in days at the time of the experiment
+- **eye**: Eye used for recording. Values: "left" or "right"
+- **prepwmorient**: Orientation of the eye in degrees. 0° indicates dorsal is toward the back of the chamber. -1 indicates unknown orientation
+- **roi_size_um2**: Area of the region of interest mask in square micrometers
+- **ventral_dorsal_pos_um** (and **field_ventral_dorsal_pos_um**): Ventral-dorsal position relative to the optic nerve in micrometers. Negative values indicate ventral location; positive values indicate dorsal location
+- **temporal_nasal_pos_um** (and **field_temporal_nasal_pos_um**): Temporal-nasal position relative to the optic nerve in micrometers. Negative values indicate temporal location; positive values indicate nasal location
+
+## Cell Type Classification
+
+- **Celltype**: Functional cell type classification according to the classifier
+- **Max_confidence**: Confidence score for the cell type classification (0-1 scale)
+- **preproc_chirp**: Preprocessed chirp average response, resampled and clipped to match the format used in Baden et al. (2016)
+- **preproc_bar**: Preprocessed moving bar response, shifted to match the format used in Baden et al. (2016)
+
+## Chirp Stimulus Responses
+
+- **chirp_on_off_index** (OOi): On-Off index from chirp stimulus. Values: +1 = On cell, -1 = Off cell, 0 = On-Off cell or non-responsive
+- **chirp_transience_index** (RTi): Response transience index. Values: +1 = very transient response, 0 = very sustained response. Negative values are not well defined
+- **chirp_qidx**: Quality index (signal-to-noise ratio) for the chirp response
+- **chirp_pres_qidx**: Percentage of cells in the field that pass the quality threshold (0.35)
+- **chirp_us_average_norm** or **chirp_60Hz_average_norm**: Resampled, normalized chirp average response at 60 Hz sampling rate
+- **chirp_us_average_dt** or **chirp_60Hz_average_dt**: Sampling interval of the upsampled chirp average (1/60 seconds)
+- **chirp_8Hz_average_norm**: Resampled, normalized chirp average response at approximately 8 Hz (7.8125 Hz). Similar to `preproc_chirp` but without reshaping to match Baden et al. (2016) format
+- **chirp_8Hz_average_dt**: Sampling interval of the 8 Hz chirp average (1/7.8125 seconds)
+- **chirp_snippets**: Chirp responses organized by repetition/trial
+- **chirp_snippets_t0**: Starting time point of each repetition
+- **chirp_snippets_dt**: Sampling interval of the snippets (0.128 seconds)
+- **chirp_triggertimes_snippets**: Trigger times for chirp snippets, required for precise temporal alignment
+
+## Moving Bar Stimulus Responses
+
+- **bar_qidx**: Quality index for moving bar response (calculated using only the preferred direction)
+- **bar_ds_index** (DSi): Direction selectivity index
+- **bar_ds_pvalue**: Statistical p-value for direction selectivity
+- **bar_pref_dir**: Preferred direction in radians
+- **bar_os_index** (OSi): Orientation selectivity index
+- **bar_os_pvalue**: Statistical p-value for orientation selectivity
+- **bar_pref_or**: Preferred orientation in radians. Note: This value is not corrected for eye orientation (left vs. right) or experimental setup geometry
+- **bar_avg_pref_dir**: Average preferred direction response at 7.81 Hz sampling rate
+
+## Receptive Fields
+
+The following fields are available when the experiment included white noise stimuli:
+
+- **rf_cdia_um**: Circle-equivalent diameter of the spatial receptive field in micrometers
+- **srf**: Spatial receptive field
+- **trf**: Temporal receptive field
+- **center_index**: Strength and sign of the RF center. Values: +1 = ON center, -1 = OFF center
+- **surround_index**: Strength and sign of the RF surround. Values: +1 = ON surround, -1 = OFF surround. Note: For meaningful analysis, the sign of the center must be taken into account
+- **split_qidx**: Quality index of the singular value decomposition (SVD) used to separate spatial and temporal components from the spatiotemporal RF
+- **rf_gauss_qidx**: Quality index of the Gaussian fit to the spatial RF
+- **polarity**: Overall polarity of the receptive field. Values: +1 = ON, -1 = OFF
+- **trf_peak_idxs**: Indices of peaks in the temporal RF
+- **relx_rf_roi_um**: Offset in setup coordinates between the ROI and RF center along the x-axis (back to front)
+- **rely_rf_roi_um**: Offset in setup coordinates between the ROI and RF center along the y-axis (left to right)
+- **tRF_tRI**: Transience index calculated from the temporal RF
+- **tRF_width**: Width of the main peak in the temporal RF
+- **tRF_lag**: Lag of the main peak in the temporal RF in seconds

README.md

@@ -55,10 +55,12 @@ For NWB documentation on accessing standard containers consult https://pynwb.rea
 
 ## 3. Reproducing the Original Analysis Table
 
+We offer companion code to reproduce the analysis in our manuscript at https://github.com/eulerlab/all-GCL-manuscript .
+
 To reproduce the original table that was used to produce visualisations and anlyses in the dataset pre-print, run:
 
 ```bash
-python export_nwb/read_nwb_table.py /path/to/target \
+python all_gcl_manuscript/read_nwb_table.py /path/to/target \
     --filter-to-match-original \
     --output reconstructed_tables # Optional, saves extracted tables in .pkl and .parquet for later access
 ```
@@ -72,7 +74,7 @@ import os
 
 import pandas as pd
 
-from all_gcl.export_nwb.utils.data_io import restore_numpy_arrays
+from all_gcl_manuscript.utils import restore_numpy_arrays
 
 dataset_path = "/path/to/data/storage"
 

Stimuli/processed_stimuli.h5

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session_Experimenter_1_2022-08-03/experiment_2_RR/field_GCL2_structure.txt

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 NWB File Structure Report
 ========================
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 ----------
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 stimulus/ (Group)
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session_Experimenter_1_2022-08-03/experiment_2_RR/field_GCL3_structure.txt

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 NWB File Structure Report
 ========================
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session_Experimenter_1_2022-08-08/experiment_1_LR/field_GCL0_structure.txt

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 NWB File Structure Report
 ========================
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session_Experimenter_1_2022-08-16/experiment_1_LR/field_GCL0.nwb

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session_Experimenter_1_2022-08-16/experiment_1_LR/field_GCL0_structure.txt

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 NWB File Structure Report
 ========================
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session_Experimenter_1_2022-08-16/experiment_1_LR/field_GCL2_structure.txt

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 NWB File Structure Report
 ========================
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session_Experimenter_1_2022-08-16/experiment_1_LR/field_GCL3_structure.txt

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 NWB File Structure Report
 ========================
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 stimulus/ (Group)
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session_Experimenter_1_2022-08-16/experiment_2_RR/field_GCL0.nwb

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session_Experimenter_1_2022-08-16/experiment_2_RR/field_GCL0_structure.txt

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 NWB File Structure Report
 ========================
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session_Experimenter_1_2022-08-16/experiment_2_RR/field_GCL1.nwb

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 NWB File Structure Report
 ========================
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