@bgicli/bgicli 2.1.1 → 2.2.0

package/data/skills/neurokit2/SKILL.md

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+---
+name: neurokit2
+description: Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
+---
+
+# NeuroKit2
+
+## Overview
+
+NeuroKit2 is a comprehensive Python toolkit for processing and analyzing physiological signals (biosignals). Use this skill to process cardiovascular, neural, autonomic, respiratory, and muscular signals for psychophysiology research, clinical applications, and human-computer interaction studies.
+
+## When to Use This Skill
+
+Apply this skill when working with:
+- **Cardiac signals**: ECG, PPG, heart rate variability (HRV), pulse analysis
+- **Brain signals**: EEG frequency bands, microstates, complexity, source localization
+- **Autonomic signals**: Electrodermal activity (EDA/GSR), skin conductance responses (SCR)
+- **Respiratory signals**: Breathing rate, respiratory variability (RRV), volume per time
+- **Muscular signals**: EMG amplitude, muscle activation detection
+- **Eye tracking**: EOG, blink detection and analysis
+- **Multi-modal integration**: Processing multiple physiological signals simultaneously
+- **Complexity analysis**: Entropy measures, fractal dimensions, nonlinear dynamics
+
+## Core Capabilities
+
+### 1. Cardiac Signal Processing (ECG/PPG)
+
+Process electrocardiogram and photoplethysmography signals for cardiovascular analysis. See `references/ecg_cardiac.md` for detailed workflows.
+
+**Primary workflows:**
+- ECG processing pipeline: cleaning → R-peak detection → delineation → quality assessment
+- HRV analysis across time, frequency, and nonlinear domains
+- PPG pulse analysis and quality assessment
+- ECG-derived respiration extraction
+
+**Key functions:**
+```python
+import neurokit2 as nk
+
+# Complete ECG processing pipeline
+signals, info = nk.ecg_process(ecg_signal, sampling_rate=1000)
+
+# Analyze ECG data (event-related or interval-related)
+analysis = nk.ecg_analyze(signals, sampling_rate=1000)
+
+# Comprehensive HRV analysis
+hrv = nk.hrv(peaks, sampling_rate=1000)  # Time, frequency, nonlinear domains
+```
+
+### 2. Heart Rate Variability Analysis
+
+Compute comprehensive HRV metrics from cardiac signals. See `references/hrv.md` for all indices and domain-specific analysis.
+
+**Supported domains:**
+- **Time domain**: SDNN, RMSSD, pNN50, SDSD, and derived metrics
+- **Frequency domain**: ULF, VLF, LF, HF, VHF power and ratios
+- **Nonlinear domain**: Poincaré plot (SD1/SD2), entropy measures, fractal dimensions
+- **Specialized**: Respiratory sinus arrhythmia (RSA), recurrence quantification analysis (RQA)
+
+**Key functions:**
+```python
+# All HRV indices at once
+hrv_indices = nk.hrv(peaks, sampling_rate=1000)
+
+# Domain-specific analysis
+hrv_time = nk.hrv_time(peaks)
+hrv_freq = nk.hrv_frequency(peaks, sampling_rate=1000)
+hrv_nonlinear = nk.hrv_nonlinear(peaks, sampling_rate=1000)
+hrv_rsa = nk.hrv_rsa(peaks, rsp_signal, sampling_rate=1000)
+```
+
+### 3. Brain Signal Analysis (EEG)
+
+Analyze electroencephalography signals for frequency power, complexity, and microstate patterns. See `references/eeg.md` for detailed workflows and MNE integration.
+
+**Primary capabilities:**
+- Frequency band power analysis (Delta, Theta, Alpha, Beta, Gamma)
+- Channel quality assessment and re-referencing
+- Source localization (sLORETA, MNE)
+- Microstate segmentation and transition dynamics
+- Global field power and dissimilarity measures
+
+**Key functions:**
+```python
+# Power analysis across frequency bands
+power = nk.eeg_power(eeg_data, sampling_rate=250, channels=['Fz', 'Cz', 'Pz'])
+
+# Microstate analysis
+microstates = nk.microstates_segment(eeg_data, n_microstates=4, method='kmod')
+static = nk.microstates_static(microstates)
+dynamic = nk.microstates_dynamic(microstates)
+```
+
+### 4. Electrodermal Activity (EDA)
+
+Process skin conductance signals for autonomic nervous system assessment. See `references/eda.md` for detailed workflows.
+
+**Primary workflows:**
+- Signal decomposition into tonic and phasic components
+- Skin conductance response (SCR) detection and analysis
+- Sympathetic nervous system index calculation
+- Autocorrelation and changepoint detection
+
+**Key functions:**
+```python
+# Complete EDA processing
+signals, info = nk.eda_process(eda_signal, sampling_rate=100)
+
+# Analyze EDA data
+analysis = nk.eda_analyze(signals, sampling_rate=100)
+
+# Sympathetic nervous system activity
+sympathetic = nk.eda_sympathetic(signals, sampling_rate=100)
+```
+
+### 5. Respiratory Signal Processing (RSP)
+
+Analyze breathing patterns and respiratory variability. See `references/rsp.md` for detailed workflows.
+
+**Primary capabilities:**
+- Respiratory rate calculation and variability analysis
+- Breathing amplitude and symmetry assessment
+- Respiratory volume per time (fMRI applications)
+- Respiratory amplitude variability (RAV)
+
+**Key functions:**
+```python
+# Complete RSP processing
+signals, info = nk.rsp_process(rsp_signal, sampling_rate=100)
+
+# Respiratory rate variability
+rrv = nk.rsp_rrv(signals, sampling_rate=100)
+
+# Respiratory volume per time
+rvt = nk.rsp_rvt(signals, sampling_rate=100)
+```
+
+### 6. Electromyography (EMG)
+
+Process muscle activity signals for activation detection and amplitude analysis. See `references/emg.md` for workflows.
+
+**Key functions:**
+```python
+# Complete EMG processing
+signals, info = nk.emg_process(emg_signal, sampling_rate=1000)
+
+# Muscle activation detection
+activation = nk.emg_activation(signals, sampling_rate=1000, method='threshold')
+```
+
+### 7. Electrooculography (EOG)
+
+Analyze eye movement and blink patterns. See `references/eog.md` for workflows.
+
+**Key functions:**
+```python
+# Complete EOG processing
+signals, info = nk.eog_process(eog_signal, sampling_rate=500)
+
+# Extract blink features
+features = nk.eog_features(signals, sampling_rate=500)
+```
+
+### 8. General Signal Processing
+
+Apply filtering, decomposition, and transformation operations to any signal. See `references/signal_processing.md` for comprehensive utilities.
+
+**Key operations:**
+- Filtering (lowpass, highpass, bandpass, bandstop)
+- Decomposition (EMD, SSA, wavelet)
+- Peak detection and correction
+- Power spectral density estimation
+- Signal interpolation and resampling
+- Autocorrelation and synchrony analysis
+
+**Key functions:**
+```python
+# Filtering
+filtered = nk.signal_filter(signal, sampling_rate=1000, lowcut=0.5, highcut=40)
+
+# Peak detection
+peaks = nk.signal_findpeaks(signal)
+
+# Power spectral density
+psd = nk.signal_psd(signal, sampling_rate=1000)
+```
+
+### 9. Complexity and Entropy Analysis
+
+Compute nonlinear dynamics, fractal dimensions, and information-theoretic measures. See `references/complexity.md` for all available metrics.
+
+**Available measures:**
+- **Entropy**: Shannon, approximate, sample, permutation, spectral, fuzzy, multiscale
+- **Fractal dimensions**: Katz, Higuchi, Petrosian, Sevcik, correlation dimension
+- **Nonlinear dynamics**: Lyapunov exponents, Lempel-Ziv complexity, recurrence quantification
+- **DFA**: Detrended fluctuation analysis, multifractal DFA
+- **Information theory**: Fisher information, mutual information
+
+**Key functions:**
+```python
+# Multiple complexity metrics at once
+complexity_indices = nk.complexity(signal, sampling_rate=1000)
+
+# Specific measures
+apen = nk.entropy_approximate(signal)
+dfa = nk.fractal_dfa(signal)
+lyap = nk.complexity_lyapunov(signal, sampling_rate=1000)
+```
+
+### 10. Event-Related Analysis
+
+Create epochs around stimulus events and analyze physiological responses. See `references/epochs_events.md` for workflows.
+
+**Primary capabilities:**
+- Epoch creation from event markers
+- Event-related averaging and visualization
+- Baseline correction options
+- Grand average computation with confidence intervals
+
+**Key functions:**
+```python
+# Find events in signal
+events = nk.events_find(trigger_signal, threshold=0.5)
+
+# Create epochs around events
+epochs = nk.epochs_create(signals, events, sampling_rate=1000,
+                          epochs_start=-0.5, epochs_end=2.0)
+
+# Average across epochs
+grand_average = nk.epochs_average(epochs)
+```
+
+### 11. Multi-Signal Integration
+
+Process multiple physiological signals simultaneously with unified output. See `references/bio_module.md` for integration workflows.
+
+**Key functions:**
+```python
+# Process multiple signals at once
+bio_signals, bio_info = nk.bio_process(
+    ecg=ecg_signal,
+    rsp=rsp_signal,
+    eda=eda_signal,
+    emg=emg_signal,
+    sampling_rate=1000
+)
+
+# Analyze all processed signals
+bio_analysis = nk.bio_analyze(bio_signals, sampling_rate=1000)
+```
+
+## Analysis Modes
+
+NeuroKit2 automatically selects between two analysis modes based on data duration:
+
+**Event-related analysis** (< 10 seconds):
+- Analyzes stimulus-locked responses
+- Epoch-based segmentation
+- Suitable for experimental paradigms with discrete trials
+
+**Interval-related analysis** (≥ 10 seconds):
+- Characterizes physiological patterns over extended periods
+- Resting state or continuous activities
+- Suitable for baseline measurements and long-term monitoring
+
+Most `*_analyze()` functions automatically choose the appropriate mode.
+
+## Installation
+
+```bash
+uv pip install neurokit2
+```
+
+For development version:
+```bash
+uv pip install https://github.com/neuropsychology/NeuroKit/zipball/dev
+```
+
+## Common Workflows
+
+### Quick Start: ECG Analysis
+```python
+import neurokit2 as nk
+
+# Load example data
+ecg = nk.ecg_simulate(duration=60, sampling_rate=1000)
+
+# Process ECG
+signals, info = nk.ecg_process(ecg, sampling_rate=1000)
+
+# Analyze HRV
+hrv = nk.hrv(info['ECG_R_Peaks'], sampling_rate=1000)
+
+# Visualize
+nk.ecg_plot(signals, info)
+```
+
+### Multi-Modal Analysis
+```python
+# Process multiple signals
+bio_signals, bio_info = nk.bio_process(
+    ecg=ecg_signal,
+    rsp=rsp_signal,
+    eda=eda_signal,
+    sampling_rate=1000
+)
+
+# Analyze all signals
+results = nk.bio_analyze(bio_signals, sampling_rate=1000)
+```
+
+### Event-Related Potential
+```python
+# Find events
+events = nk.events_find(trigger_channel, threshold=0.5)
+
+# Create epochs
+epochs = nk.epochs_create(processed_signals, events,
+                          sampling_rate=1000,
+                          epochs_start=-0.5, epochs_end=2.0)
+
+# Event-related analysis for each signal type
+ecg_epochs = nk.ecg_eventrelated(epochs)
+eda_epochs = nk.eda_eventrelated(epochs)
+```
+
+## References
+
+This skill includes comprehensive reference documentation organized by signal type and analysis method:
+
+- **ecg_cardiac.md**: ECG/PPG processing, R-peak detection, delineation, quality assessment
+- **hrv.md**: Heart rate variability indices across all domains
+- **eeg.md**: EEG analysis, frequency bands, microstates, source localization
+- **eda.md**: Electrodermal activity processing and SCR analysis
+- **rsp.md**: Respiratory signal processing and variability
+- **ppg.md**: Photoplethysmography signal analysis
+- **emg.md**: Electromyography processing and activation detection
+- **eog.md**: Electrooculography and blink analysis
+- **signal_processing.md**: General signal utilities and transformations
+- **complexity.md**: Entropy, fractal, and nonlinear measures
+- **epochs_events.md**: Event-related analysis and epoch creation
+- **bio_module.md**: Multi-signal integration workflows
+
+Load specific reference files as needed using the Read tool to access detailed function documentation and parameters.
+
+## Additional Resources
+
+- Official Documentation: https://neuropsychology.github.io/NeuroKit/
+- GitHub Repository: https://github.com/neuropsychology/NeuroKit
+- Publication: Makowski et al. (2021). NeuroKit2: A Python toolbox for neurophysiological signal processing. Behavior Research Methods. https://doi.org/10.3758/s13428-020-01516-y

package/data/skills/neuropixels-analysis/SKILL.md

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+---
+name: neuropixels-analysis
+description: "Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation."
+---
+
+# Neuropixels Data Analysis
+
+## Overview
+
+Comprehensive toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, Allen Institute, and International Brain Laboratory (IBL). Supports the full workflow from raw data to publication-ready curated units.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Working with Neuropixels recordings (.ap.bin, .lf.bin, .meta files)
+- Loading data from SpikeGLX, Open Ephys, or NWB formats
+- Preprocessing neural recordings (filtering, CAR, bad channel detection)
+- Detecting and correcting motion/drift in recordings
+- Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5)
+- Computing quality metrics (SNR, ISI violations, presence ratio)
+- Curating units using Allen/IBL criteria
+- Creating visualizations of neural data
+- Exporting results to Phy or NWB
+
+## Supported Hardware & Formats
+
+| Probe | Electrodes | Channels | Notes |
+|-------|-----------|----------|-------|
+| Neuropixels 1.0 | 960 | 384 | Requires phase_shift correction |
+| Neuropixels 2.0 (single) | 1280 | 384 | Denser geometry |
+| Neuropixels 2.0 (4-shank) | 5120 | 384 | Multi-region recording |
+
+| Format | Extension | Reader |
+|--------|-----------|--------|
+| SpikeGLX | `.ap.bin`, `.lf.bin`, `.meta` | `si.read_spikeglx()` |
+| Open Ephys | `.continuous`, `.oebin` | `si.read_openephys()` |
+| NWB | `.nwb` | `si.read_nwb()` |
+
+## Quick Start
+
+### Basic Import and Setup
+
+```python
+import spikeinterface.full as si
+import neuropixels_analysis as npa
+
+# Configure parallel processing
+job_kwargs = dict(n_jobs=-1, chunk_duration='1s', progress_bar=True)
+```
+
+### Loading Data
+
+```python
+# SpikeGLX (most common)
+recording = si.read_spikeglx('/path/to/data', stream_id='imec0.ap')
+
+# Open Ephys (common for many labs)
+recording = si.read_openephys('/path/to/Record_Node_101/')
+
+# Check available streams
+streams, ids = si.get_neo_streams('spikeglx', '/path/to/data')
+print(streams)  # ['imec0.ap', 'imec0.lf', 'nidq']
+
+# For testing with subset of data
+recording = recording.frame_slice(0, int(60 * recording.get_sampling_frequency()))
+```
+
+### Complete Pipeline (One Command)
+
+```python
+# Run full analysis pipeline
+results = npa.run_pipeline(
+    recording,
+    output_dir='output/',
+    sorter='kilosort4',
+    curation_method='allen',
+)
+
+# Access results
+sorting = results['sorting']
+metrics = results['metrics']
+labels = results['labels']
+```
+
+## Standard Analysis Workflow
+
+### 1. Preprocessing
+
+```python
+# Recommended preprocessing chain
+rec = si.highpass_filter(recording, freq_min=400)
+rec = si.phase_shift(rec)  # Required for Neuropixels 1.0
+bad_ids, _ = si.detect_bad_channels(rec)
+rec = rec.remove_channels(bad_ids)
+rec = si.common_reference(rec, operator='median')
+
+# Or use our wrapper
+rec = npa.preprocess(recording)
+```
+
+### 2. Check and Correct Drift
+
+```python
+# Check for drift (always do this!)
+motion_info = npa.estimate_motion(rec, preset='kilosort_like')
+npa.plot_drift(rec, motion_info, output='drift_map.png')
+
+# Apply correction if needed
+if motion_info['motion'].max() > 10:  # microns
+    rec = npa.correct_motion(rec, preset='nonrigid_accurate')
+```
+
+### 3. Spike Sorting
+
+```python
+# Kilosort4 (recommended, requires GPU)
+sorting = si.run_sorter('kilosort4', rec, folder='ks4_output')
+
+# CPU alternatives
+sorting = si.run_sorter('tridesclous2', rec, folder='tdc2_output')
+sorting = si.run_sorter('spykingcircus2', rec, folder='sc2_output')
+sorting = si.run_sorter('mountainsort5', rec, folder='ms5_output')
+
+# Check available sorters
+print(si.installed_sorters())
+```
+
+### 4. Postprocessing
+
+```python
+# Create analyzer and compute all extensions
+analyzer = si.create_sorting_analyzer(sorting, rec, sparse=True)
+
+analyzer.compute('random_spikes', max_spikes_per_unit=500)
+analyzer.compute('waveforms', ms_before=1.0, ms_after=2.0)
+analyzer.compute('templates', operators=['average', 'std'])
+analyzer.compute('spike_amplitudes')
+analyzer.compute('correlograms', window_ms=50.0, bin_ms=1.0)
+analyzer.compute('unit_locations', method='monopolar_triangulation')
+analyzer.compute('quality_metrics')
+
+metrics = analyzer.get_extension('quality_metrics').get_data()
+```
+
+### 5. Curation
+
+```python
+# Allen Institute criteria (conservative)
+good_units = metrics.query("""
+    presence_ratio > 0.9 and
+    isi_violations_ratio < 0.5 and
+    amplitude_cutoff < 0.1
+""").index.tolist()
+
+# Or use automated curation
+labels = npa.curate(metrics, method='allen')  # 'allen', 'ibl', 'strict'
+```
+
+### 6. AI-Assisted Curation (For Uncertain Units)
+
+When using this skill with Claude Code, Claude can directly analyze waveform plots and provide expert curation decisions. For programmatic API access:
+
+```python
+from anthropic import Anthropic
+
+# Setup API client
+client = Anthropic()
+
+# Analyze uncertain units visually
+uncertain = metrics.query('snr > 3 and snr < 8').index.tolist()
+
+for unit_id in uncertain:
+    result = npa.analyze_unit_visually(analyzer, unit_id, api_client=client)
+    print(f"Unit {unit_id}: {result['classification']}")
+    print(f"  Reasoning: {result['reasoning'][:100]}...")
+```
+
+**Claude Code Integration**: When running within Claude Code, ask Claude to examine waveform/correlogram plots directly - no API setup required.
+
+### 7. Generate Analysis Report
+
+```python
+# Generate comprehensive HTML report with visualizations
+report_dir = npa.generate_analysis_report(results, 'output/')
+# Opens report.html with summary stats, figures, and unit table
+
+# Print formatted summary to console
+npa.print_analysis_summary(results)
+```
+
+### 8. Export Results
+
+```python
+# Export to Phy for manual review
+si.export_to_phy(analyzer, output_folder='phy_export/',
+                 compute_pc_features=True, compute_amplitudes=True)
+
+# Export to NWB
+from spikeinterface.exporters import export_to_nwb
+export_to_nwb(rec, sorting, 'output.nwb')
+
+# Save quality metrics
+metrics.to_csv('quality_metrics.csv')
+```
+
+## Common Pitfalls and Best Practices
+
+1. **Always check drift** before spike sorting - drift > 10μm significantly impacts quality
+2. **Use phase_shift** for Neuropixels 1.0 probes (not needed for 2.0)
+3. **Save preprocessed data** to avoid recomputing - use `rec.save(folder='preprocessed/')`
+4. **Use GPU** for Kilosort4 - it's 10-50x faster than CPU alternatives
+5. **Review uncertain units manually** - automated curation is a starting point
+6. **Combine metrics with AI** - use metrics for clear cases, AI for borderline units
+7. **Document your thresholds** - different analyses may need different criteria
+8. **Export to Phy** for critical experiments - human oversight is valuable
+
+## Key Parameters to Adjust
+
+### Preprocessing
+- `freq_min`: Highpass cutoff (300-400 Hz typical)
+- `detect_threshold`: Bad channel detection sensitivity
+
+### Motion Correction
+- `preset`: 'kilosort_like' (fast) or 'nonrigid_accurate' (better for severe drift)
+
+### Spike Sorting (Kilosort4)
+- `batch_size`: Samples per batch (30000 default)
+- `nblocks`: Number of drift blocks (increase for long recordings)
+- `Th_learned`: Detection threshold (lower = more spikes)
+
+### Quality Metrics
+- `snr_threshold`: Signal-to-noise cutoff (3-5 typical)
+- `isi_violations_ratio`: Refractory violations (0.01-0.5)
+- `presence_ratio`: Recording coverage (0.5-0.95)
+
+## Bundled Resources
+
+### scripts/preprocess_recording.py
+Automated preprocessing script:
+```bash
+python scripts/preprocess_recording.py /path/to/data --output preprocessed/
+```
+
+### scripts/run_sorting.py
+Run spike sorting:
+```bash
+python scripts/run_sorting.py preprocessed/ --sorter kilosort4 --output sorting/
+```
+
+### scripts/compute_metrics.py
+Compute quality metrics and apply curation:
+```bash
+python scripts/compute_metrics.py sorting/ preprocessed/ --output metrics/ --curation allen
+```
+
+### scripts/export_to_phy.py
+Export to Phy for manual curation:
+```bash
+python scripts/export_to_phy.py metrics/analyzer --output phy_export/
+```
+
+### assets/analysis_template.py
+Complete analysis template. Copy and customize:
+```bash
+cp assets/analysis_template.py my_analysis.py
+# Edit parameters and run
+python my_analysis.py
+```
+
+### reference/standard_workflow.md
+Detailed step-by-step workflow with explanations for each stage.
+
+### reference/api_reference.md
+Quick function reference organized by module.
+
+### reference/plotting_guide.md
+Comprehensive visualization guide for publication-quality figures.
+
+## Detailed Reference Guides
+
+| Topic | Reference |
+|-------|-----------|
+| Full workflow | [reference/standard_workflow.md](reference/standard_workflow.md) |
+| API reference | [reference/api_reference.md](reference/api_reference.md) |
+| Plotting guide | [reference/plotting_guide.md](reference/plotting_guide.md) |
+| Preprocessing | [PREPROCESSING.md](PREPROCESSING.md) |
+| Spike sorting | [SPIKE_SORTING.md](SPIKE_SORTING.md) |
+| Motion correction | [MOTION_CORRECTION.md](MOTION_CORRECTION.md) |
+| Quality metrics | [QUALITY_METRICS.md](QUALITY_METRICS.md) |
+| Automated curation | [AUTOMATED_CURATION.md](AUTOMATED_CURATION.md) |
+| AI-assisted curation | [AI_CURATION.md](AI_CURATION.md) |
+| Waveform analysis | [ANALYSIS.md](ANALYSIS.md) |
+
+## Installation
+
+```bash
+# Core packages
+pip install spikeinterface[full] probeinterface neo
+
+# Spike sorters
+pip install kilosort          # Kilosort4 (GPU required)
+pip install spykingcircus     # SpykingCircus2 (CPU)
+pip install mountainsort5     # Mountainsort5 (CPU)
+
+# Our toolkit
+pip install neuropixels-analysis
+
+# Optional: AI curation
+pip install anthropic
+
+# Optional: IBL tools
+pip install ibl-neuropixel ibllib
+```
+
+## Project Structure
+
+```
+project/
+├── raw_data/
+│   └── recording_g0/
+│       └── recording_g0_imec0/
+│           ├── recording_g0_t0.imec0.ap.bin
+│           └── recording_g0_t0.imec0.ap.meta
+├── preprocessed/           # Saved preprocessed recording
+├── motion/                 # Motion estimation results
+├── sorting_output/         # Spike sorter output
+├── analyzer/               # SortingAnalyzer (waveforms, metrics)
+├── phy_export/             # For manual curation
+├── ai_curation/            # AI analysis reports
+└── results/
+    ├── quality_metrics.csv
+    ├── curation_labels.json
+    └── output.nwb
+```
+
+## Additional Resources
+
+- **SpikeInterface Docs**: https://spikeinterface.readthedocs.io/
+- **Neuropixels Tutorial**: https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_neuropixels.html
+- **Kilosort4 GitHub**: https://github.com/MouseLand/Kilosort
+- **IBL Neuropixel Tools**: https://github.com/int-brain-lab/ibl-neuropixel
+- **Allen Institute ecephys**: https://github.com/AllenInstitute/ecephys_spike_sorting
+- **Bombcell (Automated QC)**: https://github.com/Julie-Fabre/bombcell
+- **SpikeAgent (AI Curation)**: https://github.com/SpikeAgent/SpikeAgent