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Standardized Workflows (II)

Standardized Workflows (II). Carlos Oscar Sorzano Techn . Director I 2 PC Natl . Center Biotechnology (CSIC). Interchange Points need an interchange standard. Specific proposal in the discussion. Some interchange points. CTF estimation of micrographs :

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Standardized Workflows (II)

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  1. Standardized Workflows (II) Carlos Oscar Sorzano Techn. Director I2PC Natl. Center Biotechnology (CSIC)

  2. InterchangePointsneedaninterchangestandard Specificproposal in thediscussion

  3. Someinterchangepoints • CTF estimation of micrographs: • List of Micrograph, Voltage, DefocusU, DefocusV, AngleUX, Cs • Particle picking: • List of Micrograph, micrographXcoor, micrographYcoor • Particle extraction: • List of images • 2D Alignment/Classification: • 3D Alignment/Classification: • List of image/volume [2D or 3D alignment] • [A list of classrepresentatives] • [Classrepresentativeassignment]

  4. InterchangeProposal • Interchangeinformation: • Data: images, volumes and stacks • MetaData: list of … • Data structure • Data: Array of real values with X varyingfaster • MetaData: Table with specificcolumnnames • Data format • Data: MRC file • MetaData: STAR file with specificblocknames

  5. Data: Images, volumes and stacks .mrc MRC 2D image .mrc MRC 3D image (can be distinguishedfrom 2D byheader) .mrcs MRC Stack of 2D images Heymann, J. B.; Chagoyen, M. & Belnap, D. M.J. Structural Biology, 2005, 151, 196-207 y y (0,0) x x (0,0)

  6. MetaData: Interchangeformat

  7. MetaData: Components • UID: UniqueIdentifier • Micrograph (oneormanymotifs) • Image (motif of interest) • Volume • CTF • Coordinates • 2D Alignment • 3D Alignment • Comment

  8. MetaData: UID, Micrograph, Comment Anyentry in themetadata file has a uniqueentrynumber listOfMicrographs.3dem: # 3DEM_STAR_1General file comment # data_block_1 loop_ _UID _micrographLocator _comment 1 InputData/micrograph1.mrc “Comment 1” 2 InputData/micrograph2.mrc “Comment 2” data_block_2 loop_ _UID _micrographLocator 3 InputData/micrographA.mrc 4 InputData/micrographB.mrc

  9. MetaData: CTF Anyentry in themetadata file has a uniqueentrynumber listOCTFs.3dem: # 3DEM_STAR_1 * # data_block_1 loop_ _UID _Voltage _DefocusU _DefocusV _AngleUX _Cs 1 200 1.50 1.54 30.0 2.0 Y (in kV) (in μm) (in μm) (in degrees) (in mm.) V U X

  10. MetaData: Images and Volumes Images can be in individual files (mrc) orstacks (mrcs). Volumes are in individual files (mrc). listOfImages.3dem: # 3DEM_STAR_1 * # data_block loop_ _UID _imageLocator 1 image00001.mrc 2 image00002.mrc 3 1@stack.mrcs 4 2@stack.mrcs listOfVolumes.3dem: # 3DEM_STAR_1 * # data_block loop_ _UID _volumeLocator 1 volume00001.mrc 2 volume00002.mrc

  11. MetaData: Coordinates y listOfCoordinates.3dem: # 3DEM_STAR_1 * # data_block loop_ _UID _micrographXcoor _micrographYcoor 1 500 1000 2 750 2500 (0,0) x Heymann, J. B.; Chagoyen, M. & Belnap, D. M.J. Structural Biology, 2005, 151, 196-207

  12. MetaData: 2D Alignment 1@img.mrcs 2@img.mrcs 3@img.mrcs Δψ=60° y Δx=+5 Δy=-15 x listOfAlignedImages.3dem: # 3DEM_STAR_1 * # data_block loop_ _UID _imageLocator _imageXOff _imageYOff _imagePsiOff 1 1@img.mrcs 0 0 0 2 2@img.mrcs 5 -15 0 3 3@img.mrcs 5 -15 60

  13. MetaData: 2D Alignment 1@img.mrcs 4@img.mrcs Δψ=60° y Δx=+5 flip Δy=-15 x listOfAlignedImages.3dem: # 3DEM_STAR_1 * # data_alignedImageList_A loop_ _UID _imageLocator _imageXOff _imageYOff _imagePsiOff _imageFlip 1 1@img.mrcs 0 0 0 0 2 4@img.mrcs 5 -15 60 1

  14. MetaData: 2D Alignment 1@img.mrcs 4@img.mrcs Δψ=60° y Δx=+5 flip Δy=-15 x

  15. MetaData: 3D Alignment List of 3D aligned images.3dem: # 3DEM_STAR_1 * # data_block loop_ _UID _imageLocator _homogeneousEulerMatrix I1 mage00001.mrc [a11 a12 a13 Xoff a21 a22 a23 Yoff a31 a32 a33 0] Heymann, J. B.; Chagoyen, M. & Belnap, D. M.J. Structural Biology, 2005, 151, 196-207 List of 3D aligned volumes.3dem: # 3DEM_STAR_1 * # data_block loop_ _UID _volumeLocator _homogeneousEulerMatrix 1 volume00001.mrc [a11 a12 a13 Xoff a21 a22 a23 Yoff a31 a32 a33 Zoff]

  16. MetaData: Relationships listOfImagesAndDownsampledImages.3dem: # 3DEM_STAR_1 * # data_fullSize_images loop_ _UID _imageLocator 1 1@stack.mrcs 2 2@stack.mrcs data_downsampledSize_images loop_ _UID _imageLocator 3 1@downsampledStack.mrcs 4 2@downsampledStack.mrcs data_correspondingDownsampleImage loop_ _UID _UID1 _UID2 5 1 3 6 2 4

  17. MetaData: Interchangeformat • There can be anynumber of blockswithin a Star file. • Eachblock can combine anynumber of components • Examples: • Micrograph and locations: • micrographLocator, micrographXcoor, micrographYcoor • Micrograph and CTF: • micrographLocator, Voltage, DefocusU, DefocusV, AngleUX, Cs • Micrograph, image, locationand CTF: • micrographLocator, imageLocator, • micrographXcoor, micrographYcoor, • Voltage, DefocusU, DefocusV, AngleUX, Cs

  18. Someinterchangepoints • CTF estimation of micrographs: • Blockname: micrographCTFs • micrographLocator, Voltage, DefocusU, DefocusV, AngleUX, Cs • Particle picking: • Blockname: particlePicking • micrographLocator, micrographXcoor, micrographYcoor • Particle extraction: • Blockname: imageList • imageLocator • 2D Alignment/Classification: • 3D Alignment/Classification: • A block per class: class_00001, class_00002, … • Classblocks: imageLocator[2D or 3D alignment] • [A block of classrepresentatives] • Blockname: class_representatives • imageLocator • [Classrepresentativeassignment] • Blockname: class_representative_assignment • UID1, UID2

  19. Howtocheck? Automaticcheck of results Syntactically and Semantically

  20. Discussion • Isthisthecorrectstrategy? (interchangepoints+ interchangeformat) • Whichinterchangepoints? • Whichinterchangeformat? • Howtoreach a standard?

  21. Interchangeobjects CTF determination Micrographscreening Particle picking Micrographphasecorrection Particle extraction and screening 2D alignment and classification Initialvolumeconstruction 3D Modelrefinement 3D Modelamplitudecorrection

  22. What do wewanttointerchange? • Whatistheminimumamount of informationneeded? • How are wegoingtostoreit?

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