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Xmipp 3.0 A complete redesign

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  1. Xmipp 3.0A complete redesign

  2. PackageOverview

  3. Xmipp 1.X

  4. Xmipp2.X

  5. Xmipp 2.X: protocol

  6. Xmipp3.X

  7. Xmipp3.X

  8. Xmipp3.X • Traceability • Protocols can be monitored • Protocolsselfreport status • Protocols can be easily moved • Protocol output isstandardized • Easyaccesstoqueues • Job monitoring (local/queue) • Job stopping • Job restarting • Modification of previousparameters • More protocols • Better structured protocols • More efficient in space • More efficient in time (70% faster) • More efficient in code • Any program is a protocol • Explorer allows visualization of the whole directory tree with Xmippsemantics • Common interface sections • Semantic file selectors • Optional sections are not displayed • Better programming environment

  9. Xmipp 3.X 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

  10. Xmipp: An Image Processing Package

  11. Xmipp: An Image Processing Package

  12. Towards High-Throughput

  13. Documentation http://xmipp.cnb.csic.es

  14. Programs

  15. Programs http://xmipp.cnb.csic.es

  16. Programs General documentation of theprogram • Parameters: • Blueparameters are compulsory • Greenparameters are optional Examples and typical uses You can addyourowncomments!!

  17. Program help • Usage: brief description • - More detailed (--more) • See Also: related programs • Examples and notes

  18. Program command line interface • Common style • Color coding: • Mandatory (Blue) • Optional (Green) • Exclusivity • Requirements • Option by sections • List options

  19. Program command line interface • Arguments checking

  20. Program Graphical Interface • Use option (--gui)

  21. Program command line interface • -i argument label optional if declared first • Common options

  22. How to find a program? Search for programscontainingthekeywords‘classify' xmipp_aproposclassify Search for programscontainingthekeywords 'gaussian' and 'noise' xmipp_aproposgaussiannoise Listallxmippprograms xmipp_apropos--list Listallxmippmetadatalabels xmipp_apropos --list -t labels

  23. File formats

  24. Image formats

  25. Image formats: stacks • Several images/volumesin a file

  26. Image formats: stacks • Direct access to a single image in a stack: “@”

  27. Image formats: xmipp_image_convert • Format conversions among independent images, volumes and stack • Substitute images in stacks • Append images to stack • Put volumes in a stack of volumes • Change data type • - Adjust the histogram to the gray level range • Swap the endianness of the file

  28. Image formats: xmipp_image_convert

  29. Metadatas • File to share information between programs based on STAR format: flexible and easily extensible text archive file; it is human and machine readable and can be edited with a text editor. # XMIPP_STAR_1 * # data_fullSize_images loop_ _image _Xcoor _Ycoor 1@stack.mrcs 345 567 2@stack.mrcs 789 123

  30. Metadatas: labels • Accepted labels can be checked in example files and xmipp_apropos xmipp_apropos --list -t labels

  31. Metadatas: Example files • Programs include in Examples section a link to an example file

  32. Metadatas: xmipp_metadata_import

  33. Metadatas: xmipp_metadata_utilities • Operation between metadatas: union, subtraction, intersection, join,… • Operation on columns: sort, fill, randomize, addition, droping… • Some operations over image files in metadatas: moving,deleting… • Create queries as a database • Fill values in columns: constant, linear, random, custom modifications,…

  34. Workflows

  35. Workflow 1: Micrographstoparticles Importmicrographs Screenmicrographs Manual picking [Supervisedpicking] [Automaticpicking] Extractparticles [Preprocessparticles] Importparticles Screenparticles

  36. Workflow 1: Micrographscreening

  37. Workflow 1: Particle picking

  38. Workflow 1: Micrographstoparticles

  39. Workflow 2: 2D Classification Particles CL2D RotSpectra ML2D KerdenSOM Align 2D

  40. Workflow 3: 3D Reconstruction Particles& Micrographs Reference Volume[s] RandomConicalTilt Particles [CTF] Modelrefinement [ML3D] Output Volumes

  41. Project interface

  42. Project interface Youmaychoosetheprotocoltoexecute with thesebuttons Thisarea shows alltherunsperformed, and their status. Thisareasummarizesthe input, output and status of a protocol. Followthe links togointothedirectories

  43. Project interface Use thesebuttonstoduplicate a run, deleteitorseetherundependencies

  44. Project interface Anexample of howthedifferentstepshavebeenapplied and theirdependencies

  45. Project interface Doubleclick

  46. Project interface Thisbuttonallowsvisualization on thefly Choosethedesiredanalysisoptions Thisbuttonallowstoanalyzethe output of eachrun

  47. Project interface Whenanalyzingresults, rightclicktosee more options. For instance, torecalculatethe CTF or show the CTF profile

  48. Project interface Thisbutton shows allcommandsissuedand theconsole output of theprograms

  49. Project interface Browsetheprojectdirectory Basic objectinformation Add a filtertoeasilylocate a given file

  50. Project interface Create a new protocolrunbyselectingthedesiredaction