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Information Interchange

Information Interchange. José María Carazo Director I 2 PC Natl . Center Biotechnology (CSIC). Photo time!. To celebrate the agreement on Information Interchange …… Please do not run away at coffee time, but stay for a photography at the stairs.

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Information Interchange

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  1. Information Interchange José María Carazo Director I2PC Natl. Center Biotechnology (CSIC)

  2. Photo time! • TocelebratetheagreementonInformationInterchange…… • Please do notrunaway at coffee time, butstayfor a photography at thestairs

  3. Basic types of metadatato be interchanged • (Labels, Values) (no formatsyet!) • List of coordinates • Imagename, (x, y) pairs in pixels, samplingrate • CTF specification • Imagename, Focus, astismatism, microscope-parameters • Alignment(rotations and translations,2D and 3d) • Imagename, Homogenousmatrix

  4. Concrete case • List of coordinates • ImageIdentifier (index @ file name (string), starting at 1 (integer)) • MicrographIdentifier (index @ file name (string), starting at 1 (integer)) (if a single file name, no index) • Class_identifier (string) • Xcoorin pixels (float, origin at the center of a pixel, at the center of the box) • Ycoorin pixels () • Comment (string) • Figure of Merit (Float, range (0,1), 0 islowestquality) • ActiveFlag (binary, 0 is non-active) • Type of file (MRC, Spider, Imagic, HDF….

  5. Concrete case continued • CTF specification • DefocusU (in A. as a float, underfocus positive) • DefocusV (in A. as a float) • Angle_DefUAxis_Xaxis (in degrees, counterclockwisefrom X to U, as float) • Amplitude_Contrast (float,range (0,1)).Provideexpl. Equation in thedefinition) • Voltage (Kilo volts, as a float, non relativistic) • CS (millimeters, as a float) • Magnification (float, absolute) • Detector_spacing(float, microns per pixel)

  6. Concrete case continued • 2D/3D alignement • TransformationMatrix_a11 • TransformationMatrix_a12 • TransformationMatrix_a13 • TransformationMatrix_Xoff (float, pixels) • …..If no entryexits, is 0 (6 numbersonlyfor 2D)

  7. OnConventions • FollowingHeymann et al. • Volunteersto define a “Convention Web” tocheckthatthedifferentpackagesinterchangetheinformationaccordingtothoseconventions • Itisnecessarytospecify in the CW the CTF equationthatwehaveusedforthespecification AND thetransformationmatrixdetails • Tohavethe CW in THREE MONTHS

  8. Onformats Basic possibilities: • XML • Star • GO FOR STAR • There are I/O libreries «industryfriendly» • Further specifications to be defined by the “Convention Web Group” (in three months)

  9. DATA to be interchanged • Images, Volumes, ImageStacks, VolumeStacks • Threepossibleapproaches: • MRC format, leavingundefinedVolumeStacks • HDF for 2D/3D/4D Arrays (withdimensions and data type) • Ad hoc approaches (FLAT FILE, One dimensional of floatswith no header • CONSENSUS APROACH AFTER VOTING: Using MRC fornow, whileactivelyexploring HDF (dueto performance concerns)

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