Videre Analysis & Visualization

Overview#

Videre is NeuroNexus' analysis and visualization application within the Radiens Clarity platform. Designed for file-based neural data exploration, Videre provides interactive 3D visualization, flexible analysis pipelines, and seamless format compatibility without requiring data conversion.

Core Capabilities#

3D Visualization#

Interactive three-dimensional probe views and spatial data mapping for intuitive understanding of recording geometry and neural activity patterns.

Features:

• Real-time 3D probe rendering with anatomical context
• Interactive rotation, zoom, and pan controls
• Channel-to-site mapping visualization
• Activity-based color mapping on probe geometry
• Multi-probe spatial relationships
• Anatomical atlas integration for brain region overlay
• Custom probe geometry import and visualization
• Export 3D views for publication-quality figures

Universal Format Compatibility#

Open any neural data format without conversion, preserving original data fidelity and eliminating preprocessing bottlenecks.

Supported Formats:

• .xdat (NeuroNexus native)
• .rhd, .rhs (Intan RHD/RHS systems)
• .continuous, .dat, .events (Open Ephys)
• .nwb (Neurodata Without Borders)
• .hdf5 (Hierarchical Data Format)
• .pl2, .plx (Plexon)
• .nex, .nex5 (NeuroExplorer)
• .nsx, .nev (Blackrock Neuroport)
• .tdms, .tev, .tsq (Tucker-Davis Technologies)
• .mcd, .msrd (Multi-Channel Systems)
• .mat (MATLAB)
• .csv, .txt (Generic text formats)
• .phy, .kilosort (Spike sorting outputs)
• .spikes, .clusters (Spike train formats)

Custom Analytics#

Extensible analysis pipelines with built-in algorithms and support for custom processing workflows.

Analysis Tools:

• Spike sorting integration (Kilosort, MountainSort, SpyKING CIRCUS)
• Local field potential (LFP) analysis and spectral decomposition
• Multi-unit activity (MUA) detection and quantification
• Cross-correlation and coherence analysis
• Phase-amplitude coupling
• Spike-triggered averaging
• Burst detection and characterization
• Network connectivity analysis
• Dimensionality reduction (PCA, t-SNE, UMAP)
• Custom Python script integration via RadiensPy

Interactive Plots#

Dynamic, responsive visualizations optimized for exploratory data analysis and hypothesis generation.

Visualization Types:

• Multi-channel waveform displays with zoom and scroll
• Raster plots with trial alignment and sorting
• Peri-stimulus time histograms (PSTH)
• Power spectral density (PSD) plots
• Spectrograms and time-frequency representations
• Cross-correlograms for spike train relationships
• Firing rate maps and tuning curves
• Population vectors and state-space trajectories
• Heatmaps for matrix data (correlation, similarity)
• Interactive linked plots for coordinated exploration

Key Advantages#

1. Universal Format Compatibility#

Open 20+ neural data formats directly without conversion—.xdat, .rhd, .rhs, .nwb, .hdf5, .pl2, .plx, .nsx, .nev, .tsq, .tev, .mat, .csv, .continuous, .dat, .phy, .kilosort, and more. No preprocessing scripts, no format converters, no data copying. Point at files and start analysis immediately, regardless of acquisition system or legacy data formats.

2. Zero Preprocessing Required#

No data migration, reorganization, or conversion necessary. Videre reads files directly from their original locations with lazy loading—process multi-gigabyte datasets without consuming equivalent RAM. Preserve original data integrity while exploring multiple analysis approaches without duplicating storage.

3. Interactive 3D Visualization#

Intuitive probe geometry and activity mapping with real-time 3D rendering. Rotate, zoom, and pan through recording sites with activity-based color mapping. Immediate spatial understanding of recording configuration and neural activity patterns. Anatomical atlas integration for brain region context. Export publication-quality 3D views for figures and presentations.

4. Extensible Analysis Pipelines#

Built-in integration with Kilosort, MountainSort, SpyKING CIRCUS for spike sorting, plus custom Python script support via RadiensPy. Combine GUI-based exploration with programmatic batch processing. Template pipelines for common analyses accelerate workflow setup. Save and share pipeline configurations across lab members for consistency.

5. Publication-Ready Export#

Generate publication-quality figures directly from Videre visualizations—vector graphics (PDF, SVG, EPS) and high-resolution raster formats (PNG, TIFF) with customizable DPI, themes, fonts, and colors. Batch export multiple views with consistent styling. Eliminate post-processing in separate graphics software.

6. GPU-Accelerated Performance#

Responsive interactive rendering of 256+ channel datasets with GPU acceleration. Sub-100ms UI latency for smooth exploration even with high-density probes. Real-time waveform streaming for file review. Memory-efficient streaming handles datasets larger than available RAM without performance degradation.

Integration with Radiens Platform#

Videre operates as the analysis and exploration layer within the unified Radiens ecosystem:

• Data Sources: Direct access to files from Allego recordings or imported datasets
• Workflow Continuity: Metadata from Allego flows seamlessly into Videre analysis
• Curation Integration: Results and annotations sync with Curate for reproducible workflows
• Cloud Scaling: Heavy analysis jobs can be offloaded to Summa for distributed computing
• API Access: Full programmatic control via RadiensPy Python API

Technical Specifications#

Performance:

• Interactive rendering of 256+ channel datasets
• Real-time waveform streaming for file review
• GPU-accelerated visualization for high-density probes
• Lazy-loading for multi-gigabyte files
• Responsive UI with sub-100ms interaction latency

Platforms:

• Windows 10/11
• macOS 12+
• Ubuntu 20.04+ (with GPU support)

System Requirements:

• CPU: Intel Core i7 or AMD Ryzen 7 (8th gen or newer)
• RAM: 16 GB minimum, 32 GB recommended for large datasets
• GPU: Dedicated GPU with 4GB+ VRAM recommended for 128+ channels
• Storage: SSD for responsive file access
• Display: 1920×1080 minimum, dual monitors recommended

Analysis Workflows#

Signal Quality Assessment#

Comprehensive quality control tools for validating recording integrity.

QC Metrics:

• Per-channel signal-to-noise ratio (SNR) calculation
• Impedance trajectory analysis
• Artifact detection and quantification
• Dead channel identification
• Cross-talk analysis between channels
• Temporal drift assessment
• Statistical outlier detection

Spike Sorting#

Integrated spike sorting with manual curation and quality metrics.

Capabilities:

• Direct integration with Kilosort 2.5/3.0
• MountainSort and SpyKING CIRCUS support
• Manual cluster curation interface
• Isolation quality metrics (ISI violations, SNR, amplitude)
• Spike waveform visualization and comparison
• Drift correction for chronic recordings
• Multi-unit distinction and single-unit validation

Local Field Potential (LFP) Analysis#

Comprehensive tools for low-frequency signal analysis and network dynamics.

LFP Tools:

• Digital filtering with customizable bandpass parameters
• Power spectral density estimation (Welch, multitaper)
• Time-frequency analysis (wavelet, STFT)
• Phase extraction and phase-locking analysis
• Coherence analysis between channels and brain regions
• Granger causality for directed connectivity
• Current source density (CSD) analysis for laminar probes

Population Analysis#

Multi-unit and population-level analysis tools for systems neuroscience.

Population Metrics:

• Population firing rate dynamics
• Trial-averaged responses with statistics
• Neural state-space trajectories
• Dimensionality analysis (participation ratio, effective dimensionality)
• Decoder performance (Bayesian, GLM, neural networks)
• Information theory metrics (mutual information, entropy)

Visualization Features#

Customizable Display#

Tailored visualization layouts for different experimental paradigms and analysis goals.

Layout Options:

• Multi-panel arrangements with synchronized time axes
• Drag-and-drop panel organization
• Save and load custom layouts
• Template layouts for common analyses
• Full-screen mode for presentations
• Export layouts as figure panels

Publication-Quality Exports#

Generate publication-ready figures directly from Videre visualizations.

Export Formats:

• Vector graphics (PDF, SVG, EPS)
• High-resolution raster (PNG, TIFF)
• Customizable DPI and size specifications
• Theme options (light, dark, grayscale)
• Font and color customization
• Batch export for multiple views

Real-Time Filtering#

Interactive filtering for exploration without modifying source files.

Filter Types:

• Butterworth, Chebyshev, Bessel filters
• Notch filters for line noise removal
• Median filtering for spike extraction
• Wavelet denoising
• Artifact rejection and blanking
• Zero-phase filtering options

Advanced Features#

Multi-Session Comparison#

Compare neural activity across recording sessions for longitudinal studies.

Comparison Tools:

• Overlay waveforms from multiple sessions
• Session-to-session unit tracking
• Longitudinal stability metrics
• Batch processing across sessions
• Statistical comparison tests
• Normalized visualization for cross-session comparisons

Behavioral Integration#

Synchronize neural data with behavioral events and video streams.

Synchronization:

• Event-aligned neural responses
• Video-synchronized playback
• Trial-based segmentation
• Behavioral state coloring
• Task phase demarcation
• Closed-loop event markers

Custom Analysis Scripts#

Extend Videre functionality with Python scripts and custom algorithms.

Scripting Capabilities:

• Python API access to loaded datasets
• Custom plot generation and integration
• Batch processing automation
• Third-party library integration (NumPy, SciPy, scikit-learn)
• Export analysis results to external formats
• Template scripts for common workflows

Machine Learning Integration#

Apply modern machine learning techniques to neural data analysis.

ML Features:

• Automated spike sorting with deep learning models
• Dimensionality reduction (t-SNE, UMAP, VAE)
• Neural decoders (GLM, neural networks, SVMs)
• Cluster analysis (k-means, Gaussian mixture models)
• Anomaly detection for quality control
• Transfer learning for cross-dataset analysis

Use Cases#

Exploratory Data Analysis#

Rapidly explore datasets to identify patterns and generate hypotheses.

Benefits:

• Quick overview of recording quality and content
• Interactive exploration without scripting
• Visual pattern recognition
• Hypothesis-driven filtering and segmentation

Single-Unit Characterization#

Detailed analysis of individual neuron properties and responses.

Applications:

• Receptive field mapping
• Tuning curve generation
• Temporal response profiles
• Spike waveform characterization
• Burst and firing pattern analysis

Network Dynamics#

Population-level analysis for systems neuroscience questions.

Applications:

• Functional connectivity mapping
• Oscillation analysis and phase relationships
• Ensemble dynamics and neural trajectories
• Information flow between regions

Methods Validation#

Compare analysis approaches and validate methodological choices.

Validation Tools:

• Ground truth comparison for spike sorting
• Parameter sweep visualization
• Split-half reliability analysis
• Cross-validation metrics

Quality Control Features#

Automated QC Reports#

Generate comprehensive quality assessment reports for recordings.

Report Contents:

• Per-channel SNR and noise floor
• Spike detection statistics
• Artifact prevalence and timing
• Impedance stability
• Data completeness and dropout events
• Summary quality score

Interactive Quality Review#

Manual review interface for detailed quality assessment.

Review Tools:

• Bad channel marking and exclusion
• Artifact segment annotation
• Time period selection for analysis
• Quality notes and documentation
• Comparison with quality standards

Data Management#

Dataset Organization#

Efficient management of analysis datasets and results.

Organization Features:

• Virtual dataset collections without file copying
• Tag-based categorization
• Search and filter by metadata
• Quick access to recent analyses
• Bookmark important time segments

Result Persistence#

Save analysis results for reproducibility and collaboration.

Saved Elements:

• Analysis parameters and settings
• Generated plots and figures
• Computed metrics and statistics
• Unit classifications and annotations
• Custom filter configurations

Licensing and Availability#

License Tiers:

• Radiens BASE: Core visualization and basic analysis
• Radiens ANALYZE: Full feature set with advanced analytics
• Radiens SUITE: Videre + cloud integration via Summa

Trial Access: 30-day full-featured trial available

Updates: Regular feature updates with format compatibility expansions

Support and Documentation#

• User Guide: Comprehensive documentation for all features
• Video Tutorials: Screen recordings for common workflows
• Analysis Recipes: Step-by-step guides for standard analyses
• Python API Docs: Complete reference for scripting
• Example Datasets: Sample data for learning and testing
• Community Forum: User discussions and shared workflows
• Direct Support: Technical assistance from NeuroNexus engineers

Scientific Validation#

Videre is developed by NeuroNexus, whose products support research cited in 5,000+ publications. The analysis algorithms are validated against published methods and continuously refined based on researcher feedback from labs worldwide.

Future Roadmap#

• AI-Powered Analysis: Automated detection of neural patterns and anomalies
• Cloud Collaboration: Real-time collaborative analysis sessions
• Extended ML Models: Pre-trained models for common analysis tasks
• Enhanced 3D Rendering: VR/AR support for immersive data exploration
• Expanded Format Support: Additional proprietary and emerging formats
• Real-Time Integration: Live analysis connection with Allego acquisition