1. Information Interchange José María Carazo Director I 2 PC Natl. Center Biotechnology (CSIC)

2. 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

3. Basic types of metadata to be interchanged (Labels, Values) (no formats yet!) – List of coordinates Image name, (x, y) pairs in pixels, sampling rate – CTF specification Image name, Focus, astismatism, microscope-parameters – Alignment (rotations and translations,2D and 3d) Image name, Homogenous matrix

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) Xcoor in pixels (float, origin at the center of a pixel, at the center of the box) Ycoor in pixels () Comment (string) Figure of Merit (Float, range (0,1), 0 is lowest quality) 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, counter clock wise from X to U, as float) Amplitude_Contrast (float,range (0,1)).Provide expl. Equation in the definition) 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 entry exits, is 0 (6 numbers only for 2D)

7. On Conventions Following Heymann et al. – Volunteers to define a “Convention Web” to check that the different packages interchange the information according to those conventions – It is necessary to specify in the CW the CTF equation that we have used for the specification AND the transformation matrix details – To have the CW in THREE MONTHS

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

9. DATA to be interchanged Images, Volumes, ImageStacks, VolumeStacks – Three possible approaches: MRC format, leaving undefined VolumeStacks HDF for 2D/3D/4D Arrays (with dimensions and data type) Ad hoc approaches (FLAT FILE, One dimensional of floats with no header – CONSENSUS APROACH AFTER VOTING: Using MRC for now, while actively exploring HDF (due to performance concerns)