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Scipion: Toward software integration, reproducibility and
validation in EM image processing
Biocomputing Unit, Instruct Image Processing Center, CNB-CSIC
J.M. de la Rosa Trevín
There are different EM modalities
• Single Particles
• Helical
• 2D Crystallography
• Tomography
There is a long path to produce a 3D model
Sample Preparation
Image Acquisition
3D reconstruction
3D model2D Analysis
Image acquisition and preprocessing
Data collection
Movies alignment (with DDD)
Micrographs CTF estimation
2D image processing for Single Particles
Particle Picking
Screening - Preprocessing
Alignment and Classification
3D reconstruction
Initial model
3D classification
3D refinement
VALIDATION
The EM field needs software integration
Using different EM software packages is now like the
tower of Babel
Appion is certainly a pioneer work in terms of software integration (and our main inspiration)
It is increasing the number of external tools added to current EM packages (such as Eman2, Xmipp3 or Relion )
But still is complicated to easily use tools from different packages in one project…
Scipion goals
1. Integrate EM software packages to be used in the same project.
2. Full project traceability, improving reproducibility.
3. Execute complete workflows in an automated manner.
4. Easy to install and use.5. Easy to extend with new protocols.
Goal 1: Integrate EM software packages to be used in the same project.
All vs All is hard to maintain and extend
All conversions: N*N
New package: 2*N
It is better to have a common format
All conversions: N+N
New package: 2
We bridge across package differences by modeling our domain
3D Reconstruction
Set of Images
Initial Model
3D Volume
DataProtocols
We need conversion functions for each package
Goal 2: Full project traceability, improving reproducibility.
Results should be reproducible, not more “black boxes”
We implemented asimple storage mechanism
Mapper Layer
Data Objects
Protocol Objects
Goal 3: Execute complete workflows in an automated manner.
Scipion client
Worker Host 1 Worker Host 2
Scipion Server Bookeeping
Designed to perform distributed execution
Distributed data storage
Big data transfers
Goal 4: Easy to install and use.
Goal 5: Easy to extend with new protocols.
(Let´s see Scipion in action)
Example 1: Integration of Spider-MDA (in collaboration with Tanvir Shaikh)
Example 2: Integration of Normal Modes analysis and flexible fitting
(in collaboration with Slavica Jonic)
Example 3: Integration of ResMap
(in collaboration with Alp Kucukelbirand Hemant Tagare)
List of currently integrated Protocols: Software package and tools Protocols integrated into Scipion
Xmipp 3.1 All
Niko Grigorieff ctffind3.5/4, frealign9.07 refinement and classification
Eman 2.1 Initial model, particle picking, 3D refinement
Spider Filters, align APSR, CAPCA, classify Ward,Refinement 3D
Relion Most of programs
Bsoft Particle picking
ResMap Local resolution estimation
Dosefgpu DD Movie averaging
Roadmap 2015
May : Alpha release Pilot installations outside Madrid. (A few have been made already)
June : Beta release announcement in 3DEM list
End of summer : Scipion 1.0 release
There is a team behind
www.structuralbiology.euFollow us on twitter @instructhub