Performance Metrics
CryoSPARC Live is built and tuned for high performance pre-processing and streaming reconstruction of single particle data, and can use multiple concurrent GPUs for to maximize throughput.
CryoSPARC Live preprocessing includes four steps: (1) motion correction, (2) CTF estimation, (3) particle picking and (4) extraction.
CryoSPARC Live can sustain a throughput of 450 or more exposures per hour, per GPU, for K3 data. On a 4-GPU machine, that can scale to 1800+ exposures per hour! For K2 or Falcon data, performance can be even higher, upwards of 650 exposures per hour per GPU.
Depending on your hardware configuration (particularly raw data storage disk access speed), each preprocessing worker can sustain a throughput of at least one movie every 30 seconds, which is equal to ~2,500 movies per day per GPU.
In our internal tests, we have seen performance on well-tuned systems (like the testing hardware below) reaching up to 8,000 movies per GPU per day. See the Hardware Configurations used for Benchmarking section to see details on what hardware was used to run the benchmarks.
All 3D renderings were captured in ChimeraX from maps created by cryoSPARC Live.
All pre-processing timings were measured with Configuration 1, unless otherwise noted.
Component | Configuration 1 | Configuration 2 | Configuration 3 |
CPU | AMD Ryzen Threadripper 2950x | AMD Ryzen Threadripper 3960x | AMD Ryzen Threadripper 3960x |
Memory Bandwidth | 128 GB/s | 144GB/s | 144GB/s |
RAM | 128GB DDR4 2666MHz | 256GB DDR4 2933MHz | 256GB DDR4 2933MHz |
GPU 0 | Quadro GV100 | Quadro RTX 8000 | GeForce RTX 3090 |
GPU 1 | Quadro GV100 | Quadro RTX 8000 | GeForce RTX 3090 |
GPU 2 | Quadro RTX 5000 | GTX 1080Ti | - |
GPU 3 | GTX 1080Ti | Tesla K40c | - |
Fast CPU memory bandwidth is a major contributing factor to high performance in cryoSPARC Live. Please make note of this metric when selecting your system's CPU and RAM.
Benchmark results for 668 MRC-format uncompressed movies from a GATAN K2 4k × 4k detector. The first 40 of 100 frames were used.
Exposures from this dataset were captured with the stage tilted 40º.
Particles were selected with the Template Picker strategy. Streaming 2D Classification, Ab-initio Reconstruction and Streaming Refinement yielded 3.0Å resolution map from ~230,000 particles.
Property | Value |
Detector | Gatan K2 |
Number of Movies | 668 |
File Format | MRC |
Frame Size | 3838 x 3710 |
Frames per Movie | 100 (40 used) |
Pixel Size | 1.13Å |
Particle Extraction Box Size | 144 × 144 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 430 |
Movies Pre-processed Per Day Per GPU | 10290 |
Average Pre-processing Time Per Movie | 8.4s |
Benchmark results for ~24,000 TIFF-LZW compressed movies from a GATAN K2 4k × 4k detector.
Particles were selected with the Blob Picker strategy. Streaming 2D Classification, Ab-initio Reconstruction and Streaming Refinement yielded 3.3Å resolution map from ~300,000 particles.
Property | Value |
Detector | Gatan K2 Summit |
Number of Movies | 25084 |
File Format | TIF-LZW |
Frame Size | 3838 × 3710 |
Frames per Movie | 40 |
Pixel Size | 0.85Å |
Particle Extraction Box Size | 512 × 512 |
Particle Extraction Bin Size | 256 x 256 |
Applied Symmetry | C2 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 650 |
Movies Pre-processed Per Day Per GPU | 15600 |
Average Pre-processing Time Per Movie | 5.5s |
Benchmark results for ~200 TIFF-LZW compressed movies from a GATAN K2 detector with super-resolution capture.
Particles were selected with the Template Picker strategy. Streaming 2D Classification, Ab-initio Reconstruction and Streaming Refinement yielded a 2.5Å resolution map from ~130,000 particles.
The target T20S Proteasome has D7 symmetry.
EMPIAR-10025 T20S Proteasome at 2.8 Å Resolution
Dataset on EMPIAR
Property | Value |
Detector | Gatan K2 (super-res) |
Number of Movies | 196 |
File Format | TIFF-LZW |
Frame Size | 7420 × 7676 |
Frames per Movie | 38 |
Pixel Size | 0.6575Å |
Particle Extraction Box Size | 448 × 448 |
Applied Symmetry | D7 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 254 |
Movies Pre-processed Per Day Per GPU | 6096 |
Average Pre-processing Time Per Movie | 14.2s |
Benchmark results for ~200 TIFF-LZW compressed movies from a GATAN K3 detector. The first 40 of 64 frames were used.
Particles were selected with the Blob Picker strategy. Post-processing (2D Classification, Refinement, etc.) was not run on this dataset.
Exposures in this dataset were captured with beam-induced tilt.
Property | Value |
Detector | Gatan K3 |
Number of Movies | 3159 |
File Format | TIFF-LZW |
Frame Size | 5760 × 4092 |
Frames per Movie | 62 (40 used) |
Pixel Size | 0.826Å |
Particle Extraction Box Size | 144 × 144 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 420 |
Movies Pre-processed Per Day | 10050 |
Average Pre-processing Time Per Movie | 8.6s |
Benchmark results using super-resolution variants from super-resolution variant of previous dataset. Only the first 40 frames of each exposure were used.
Property | Value |
Detector | Gatan K3 (super-res) |
Number of Movies | 4259 |
File Format | TIFF-LZW |
Frame Size | 11520 × 8184 |
Frames per Movie | 67 (40 used) |
Pixel Size | 0.413Å |
Particle Extraction Box Size | 288 × 288 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 192 |
Movies Pre-processed Per Day Per GPU | 4608 |
Average Pre-processing Time Per Movie | 18.7s |
Benchmark results for ~3000 TIFF-LZW compressed movies from a Falcon III detector.
Particles were selected with the Blob Picker strategy. Post-processing (2D Classification, Refinement, etc.) was not run on this dataset.
Property | Value |
Detector | TFS Falcon III |
Number of Movies | 2895 |
File Format | TIFF-LZW |
Frame Size | 4096 × 4096 |
Frames per Movie | 64 |
Pixel Size | 0.835Å |
Particle Extraction Box Size | 420 × 420 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 493 |
Movies Pre-processed Per Day Per GPU | 11832 |
Average Pre-processing Time Per Movie | 7.3s |
Benchmark results for ~3000 Electron Event Representation (EER) movies from a Falcon IV detector. The particle is highly symmetric. The target apoferritin is highly symmetric. Enough information is present in the dataset to approach atomic resolution.
Particles were selected with the ring template picker strategy. Streaming 2D Classification, Ab-initio Reconstruction and Streaming Refinement yielded a 1.9Å resolution map from ~700,000 particles without any additional processing.
EMPIAR-10424 Atomic resolution structure of apoferritin
Dataset on EMPIAR
Property | Value |
Detector | TFS Falcon IV |
Number of Movies | 3370 |
File Format | EER |
Frame Size | 8192 × 8192 |
Frames per Movie | 434 (40 used) |
Pixel Size | 0.457Å |
Particle Extraction Box Size | 512 × 512 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 303 |
Movies Pre-processed Per Day Per GPU | 7272 |
Average Pre-processing Time Per Movie | 11.9s |
Benchmark results for ~3000 TIFF-LZW compressed movies from a GATAN K2 detector. The target complex is a small, flexible membrane protein.
Particles were selected with the Template Picker strategy. Streaming 2D Classification, Ab-initio Reconstruction and Streaming Refinement yielded a 3.9Å resolution map from ~700,000 particles.
Property | Value |
Detector | Gatan K2 |
Number of Movies | 2756 |
File Format | TIFF-LZW |
Frame Size | 3838 × 3710 |
Frames per Movie | 40 |
Pixel Size | 0.86Å |
Particle Extraction Box Size | 360 × 360 |
Particle Extraction Bin Size | 256 × 256 |
Metric | Value |
Movies Pre-processed Per Hour Per GPU | 870 |
Movies Pre-processed Per Day Per GPU | 20880 |
Average Pre-processing Time Per Movie | 4.13s |
Metric | Value |
Particles Extracted for 2D Classification | 79,278 |
Time to 2D Classify Extracted Particles | 4 minutes, 16 seconds |
Particles Used for Reconstruction | 100,000 |
Time to Reconstruct Initial Volume (Ab-initio) | 5 minutes, 11 seconds |
Particles Selected for Refinement | 278,312 |
Time to Refine Final Volume | 22 minutes, 55 seconds |