Performance Metrics

CryoSPARC Live 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.

Hardware Configurations Used for Benchmarking

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.

K2 MRC (HA Trimer)

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.

EMPIAR-10097 40 Degree Tilted Single-Particle CryoEM of Highly Preferred Orientated Influenza Hemagglutinin Trimerwww.ebi.ac.uk

Dataset on EMPIAR

Data Properties

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

Benchmarks

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

K2 TIFF (Nav1.7)

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.

EMPIAR-10261 CryoEM micrographs of ProTx2-bound Nav1.7 VSD2-NavAb chimeric channelwww.ebi.ac.uk

Dataset on EMPIAR

Data Properties

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

Benchmarks

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

K2 super-res TIFF (T20S)

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 Resolutionwww.ebi.ac.uk

Dataset on EMPIAR

Data Properties

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

Benchmarks

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

K3 TIFF (TT-OAD2)

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.

EMPIAR-10346 Cryo-EM of GLP-1 receptor bound to TT-OAD2 non-peptidic agonistwww.ebi.ac.uk

Dataset on EMPIAR

Data Properties

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

Benchmarks

Metric	Value
Movies Pre-processed Per Hour Per GPU	420
Movies Pre-processed Per Day	10050
Average Pre-processing Time Per Movie	8.6s

K3 super-res TIFF (TT-OAD2)

Benchmark results using super-resolution variants from super-resolution variant of previous dataset. Only the first 40 frames of each exposure were used.

Data Properties

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

Benchmarks

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

Falcon III TIFF (PAC1)

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.

EMPIAR-10351 Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G proteinwww.ebi.ac.uk

Data Properties

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

Benchmarks

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

Falcon IV EER (Apoferritin)

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 apoferritinwww.ebi.ac.uk

Dataset on EMPIAR

Data Properties

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

Benchmarks

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

K2 TIFF with Preprocessing + 2D/3D Streaming (CB1 Gi)

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.

EMPIAR-10288 Cryo electron microscopy of Cannabinoid Receptor 1-G Protein Complexwww.ebi.ac.uk

Dataset on EMPIAR

Data Properties

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

Benchmarks

Pre-processing and streaming results for this dataset measured with Hardware Configuration 3

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

Post-Processing: 256 × 256 box size, 50 2D Classes

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