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 Trimer
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 channel
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 Resolution
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 agonist
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 protein

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 apoferritin
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 Complex
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
Last modified 5mo ago