ZetaCore
A modular, high-performance processing pipeline for light-sheet fluorescence microscopy that delivers improved speed and quality.
Overview
Processing the large multi-hundred-gigabyte datasets generated by modern light-sheet fluorescence microscopy (LSFM) presents significant computational challenges, including GPU memory limitations, slow I/O, and complex image artifacts. ZetaCore is designed to overcome these challenges with efficient algorithms and resource management.
Our channel-by-channel, chunk-based workflow leverages GPU acceleration for all core processing stages while utilizing out-of-core techniques with memory-mapped files to maintain a low and constant memory footprint. This enables the efficient processing of datasets that far exceed the available system RAM or VRAM.
Performance Benchmarks
We've conducted extensive benchmarking comparing ZetaCore against existing commercial solutions for processing Zeiss lattice lightsheet microscopy data. The results speak for themselves.
Processing time comparison for losslessly compressed Zeiss CZI files. Note: on-disk file sizes are shown; actual data sizes are larger.
Benchmark hardware: Xeon Gold 6234 (8-core), 384GB DDR4 ECC RAM, NVIDIA RTX A6000 Ada (48GB VRAM), 4TB NVMe storage
Key Results: ZetaCore processes datasets 5-6 times faster. For example, a dataset that would typically take 3 days and 7 hours to process completes in under 16 hours with ZetaCore. This speedup allows researchers to iterate faster and process more data in the same timeframe.
User Interface
ZetaCore features an intuitive interface designed for ease of use while providing complete control over processing parameters.
The interface provides real-time progress monitoring, comprehensive logging, and visual feedback throughout the processing pipeline. Users can easily configure deconvolution parameters, flat-field correction settings, and output formats.
Whether you're processing a single dataset or setting up batch processing for multiple experiments, ZetaCore's interface streamlines your workflow.
ZetaCore processing interface
Technical Specifications
Key Features
- Processing Architecture: Channel-by-channel, chunk-based workflow
- GPU Acceleration: 100% GPU-accelerated core processing stages
- Memory Management: Out-of-core processing with constant memory footprint
- Flat-Field Correction: Global correction isolates hardware illumination patterns
- Deconvolution: Hybrid in-memory/out-of-core engine
- Deskewing: Fully out-of-core GPU-accelerated deskewing
- File Handling: Memory-mapped files for efficient I/O
- Supported Formats: Native support for Zeiss CZI and other common formats
System Requirements
- GPU: NVIDIA GPU with 8GB+ VRAM (16GB+ VRAM recommended)
- RAM: 32GB minimum, 64GB+ recommended
- Storage: NVMe SSD highly recommended for optimal I/O performance
- Operating System: Windows 10/11, Linux
Example Results
See the improvements ZetaCore delivers. Use the interactive sliders below to compare before and after processing. Drag the slider left and right to reveal the differences.
Deconvolution Results
Our GPU-accelerated Richardson-Lucy deconvolution improves image clarity and resolution.
Flat-Field Correction Results
Global flat-field correction eliminates hardware-induced shading artifacts and uneven illumination.
Tip: Click the "🔍 Fullscreen" button to view the comparisons in full detail!
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