Xmipp 3.0: Towards High-Throughput Single Particle Analysis

Xmipp 3.0: Towards High-Throughput Single Particle Analysis

Xmipp 3.0:
Towards High-Throughput
Single Particle Analysis
Biocomputing Unit, CNB-CSIC
Instruct Image Processing Center
Towards high-throughput
C.O.S. Sorzano, J. M. de la Rosa Trevín, J. Otón, J. J. Vega, J. Cuenca, A. Zaldívar-Peraza, J. Gómez-Blanco, J. Vargas, A. Quintana, R. Marabini, J. M. Carazo. Semiautomatic, high-throughput, high-resolution protocol for
three-dimensional reconstruction of Single Particles in Electron Microscopy. Nanoimaging: Methods and Protocols. Methods in Molecular Biology, 950: 171-193. Eds. Alioscka Sousa, Michael Kruhlak. Humana Press. (2012)
Towards high-throughput
C.O.S. Sorzano, J. M. de la Rosa Trevín, J. Otón, J. J. Vega, J. Cuenca, A. Zaldívar-Peraza, J. Gómez-Blanco, J. Vargas, A. Quintana, R. Marabini, J. M. Carazo. Semiautomatic, high-throughput, high-resolution protocol for
three-dimensional reconstruction of Single Particles in Electron Microscopy. Nanoimaging: Methods and Protocols. Methods in Molecular Biology, 950: 171-193. Eds. Alioscka Sousa, Michael Kruhlak. Humana Press. (2012)
Towards high-throughput
C.O.S. Sorzano, J. M. de la Rosa Trevín, J. Otón, J. J. Vega, J. Cuenca, A. Zaldívar-Peraza, J. Gómez-Blanco, J. Vargas, A. Quintana, R. Marabini, J. M. Carazo. Semiautomatic, high-throughput, high-resolution protocol for
three-dimensional reconstruction of Single Particles in Electron Microscopy. Nanoimaging: Methods and Protocols. Methods in Molecular Biology, 950: 171-193. Eds. Alioscka Sousa, Michael Kruhlak. Humana Press. (2012)
Towards High-Throughput
Process
Time
Micrograph screening
15 min.
Semi automatic particle picking
50 min.
(+1 h. manual training and revision)
Particle screening
3 min.
Particle downscaling
3 min.
CL2D
6 h.
Initial volume construction
3 min.
3D Model refinement Iterations 1-11
13 h.
(phase corrected)
Amplitude correction via B-factor
2 min.
Total
<24h
Xmipp, a bit of history
Image processing for electron microscopy using
Xmipp: An Image Processing Package for
XMIPP
Electron Microscopy
2013
2004
2008
1996
XMIPP: A new generation of an open-source
Image Processing Package for Electron
Microscopy
XMIPP 3.0
Xmipp 1.X
Xmipp 2.X
Xmipp 2.X
Xmipp 3.0
Xmipp
Xmipp Main Features:
•
Advanced image processing: Xmipp has the most advanced image processing algorithms adapted to
EM needs.
•
Reliable: based on theory and taking care of data.
•
High performance: exploit CPU and parallel power.
•
Continuous development: bug fixes, improvements, new features.
•
Easy to use: easy installation, intuitive GUI, good data analysis.
•
Interoperable: can read many image formats.
•
Traceability/Reproducibility: all parameters and steps are saved.
•
Well documented: for users and developers
Xmipp 3.0 in use
http://xmipp.cnb.csic.es
Documentation
Documentation
Image formats
Image Processing Workflows
Image Processing Workflows
Image Processing Workflows
Image Processing Workflows
Xmipp 3.0 Project GUI
Analyze results
Output files
Parameters form
Wizard example
Custom file browser
Particle picking
CTF Profiles
Volume display
Data visualization
Data visualization
ImageJ integration
Other improvements not
seen by users
Code has been optimized,
now is 60% faster than
Before → Time saving
We can handle more image formats for I/O,
including stacks → Disk space saving
Files can be read in memory or disk → Memory saving
Algorithms
Conclusions
Project management improves workflow traceability through the organization of protocols, runs and steps.
Graphical interfaces are now richer and more flexible than before.
Image formats support has been extended to cover most of the formats used in the field
Standardization of results allows a better interaction between different Xmipp programs as well as with external
applications.
Software design has been improved. Code is more organized, tested and optimized; programs are up to 50 percent
faster.
The team