standardized workflows (ii) carlos oscar sorzano techn. director i 2 pc natl. center biotechnology...
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Standardized Workflows (II)
Carlos Oscar SorzanoTechn. Director I2PC
Natl. Center Biotechnology (CSIC)
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Interchange Points needan interchange standard
Specific proposal in the discussion
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Some interchange points• 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 class representatives]• [Class representative assignment]
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Interchange Proposal• Interchange information:– Data: images, volumes and stacks– MetaData: list of …
• Data structure– Data: Array of real values with X varying faster– MetaData: Table with specific column names
• Data format– Data: MRC file– MetaData: STAR file with specific block names
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Data: Images, volumes and stacks.mrc MRC 2D image.mrc MRC 3D image (can be distinguished from 2D by header).mrcs MRC Stack of 2D images
Heymann, J. B.; Chagoyen, M. & Belnap, D. M.J. Structural Biology, 2005, 151, 196-207
Header Val0 Val1 ValN
ValN
Val0 Val1
x
y
(0,0)x
y
(0,0)
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MetaData: Interchange format
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MetaData: Components
• UID: Unique Identifier• Micrograph (one or many motifs)• Image (motif of interest)• Volume• CTF• Coordinates• 2D Alignment• 3D Alignment• Comment
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MetaData: UID, Micrograph, CommentAny entry in the metadata file has a unique entry number
listOfMicrographs.3dem:# 3DEM_STAR_1 General file comment # data_block_1loop_ _UID _micrographLocator _comment1 InputData/micrograph1.mrc “Comment 1” 2 InputData/micrograph2.mrc “Comment 2”data_block_2loop_ _UID _micrographLocator3 InputData/micrographA.mrc 4 InputData/micrographB.mrc
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MetaData: CTFAny entry in the metadata file has a unique entry number
listOCTFs.3dem:# 3DEM_STAR_1 *# data_block_1loop_ _UID _Voltage _DefocusU _DefocusV _AngleUX _Cs1 200 1.50 1.54 30.0 2.0
(in kV)(in μm)(in μm)
(in degrees)(in mm.) X
Y
UV
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MetaData: Images and VolumesImages can be in individual files (mrc) or stacks (mrcs).Volumes are in individual files (mrc).
listOfImages.3dem:# 3DEM_STAR_1 * # data_blockloop_ _UID _imageLocator1 image00001.mrc 2 image00002.mrc3 [email protected] [email protected]
listOfVolumes.3dem:# 3DEM_STAR_1 * # data_blockloop_ _UID _volumeLocator1 volume00001.mrc 2 volume00002.mrc
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MetaData: Coordinates
Heymann, J. B.; Chagoyen, M. & Belnap, D. M.J. Structural Biology, 2005, 151, 196-207
x
y
(0,0)
listOfCoordinates.3dem:# 3DEM_STAR_1 * # data_blockloop_ _UID _micrographXcoor _micrographYcoor1 500 10002 750 2500
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MetaData: 2D Alignment
x
y Δx=+5
Δy=-15
Δψ=60°
[email protected] [email protected] [email protected]
listOfAlignedImages.3dem:# 3DEM_STAR_1 * # data_blockloop_ _UID _imageLocator _imageXOff _imageYOff _imagePsiOff1 [email protected] 0 0 02 [email protected] 5 -15 03 [email protected] 5 -15 60
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MetaData: 2D Alignment
x
y
listOfAlignedImages.3dem:# 3DEM_STAR_1 * # data_alignedImageList_Aloop_ _UID _imageLocator _imageXOff _imageYOff _imagePsiOff _imageFlip1 [email protected] 0 0 0 02 [email protected] 5 -15 60 1
Δx=+5
Δy=-15
Δψ=60°
flip
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MetaData: 2D Alignment
x
y
Δx=+5
Δy=-15
Δψ=60°
flip
14 1( ) ( )I I Rr r
1
x
y
r
cos sin
sin cos
0 0 1
x
R m m m y
1,1m
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MetaData: 3D AlignmentList of 3D aligned images.3dem:# 3DEM_STAR_1 * # data_blockloop_ _UID _imageLocator _homogeneousEulerMatrixI1 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_blockloop_ _UID _volumeLocator _homogeneousEulerMatrix1 volume00001.mrc [a11 a12 a13 Xoff a21 a22 a23 Yoff a31 a32 a33 Zoff]
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MetaData: RelationshipslistOfImagesAndDownsampledImages.3dem:# 3DEM_STAR_1 * # data_fullSize_imagesloop_ _UID _imageLocator1 [email protected] [email protected]_downsampledSize_imagesloop_ _UID _imageLocator3 [email protected] [email protected]_correspondingDownsampleImageloop_ _UID _UID1 _UID25 1 36 2 4
1 2RUID UID
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MetaData: Interchange format
• There can be any number of blocks within a Star file.• Each block can combine any number of components• Examples:
• Micrograph and locations:micrographLocator, micrographXcoor, micrographYcoor
• Micrograph and CTF:micrographLocator, Voltage, DefocusU, DefocusV, AngleUX, Cs
• Micrograph, image, location and CTF:micrographLocator, imageLocator,
micrographXcoor, micrographYcoor , Voltage, DefocusU, DefocusV, AngleUX, Cs
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Some interchange points• CTF estimation of micrographs:
• Block name: micrographCTFs• micrographLocator, Voltage, DefocusU, DefocusV, AngleUX, Cs
• Particle picking:• Block name: particlePicking• micrographLocator, micrographXcoor, micrographYcoor
• Particle extraction:• Block name: imageList• imageLocator
• 2D Alignment/Classification:• 3D Alignment/Classification:
• A block per class: class_00001, class_00002, …• Class blocks: imageLocator [2D or 3D alignment]
• [A block of class representatives]• Blockname: class_representatives• imageLocator
• [Class representative assignment]• Blockname: class_representative_assignment• UID1, UID2
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How to check?
Automatic check of results
Syntactically and Semantically
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Discussion
• Is this the correct strategy? (interchange points + interchange format)
• Which interchange points?• Which interchange format?• How to reach a standard?
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Interchange objectsCTF determination
Micrograph screening
Particle picking
Particle extraction and screening
2D alignment and classification
Initial volume construction
3D Model refinement
Micrograph phase correction
3D Model amplitude correction
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• What do we want to interchange?• What is the minimum amount of information
needed?• How are we going to store it?