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Automated data collection

Automated data collection. Peter Zwart Berkeley Center for Structural Biology Physical Biosciences Division, LBL. Automated data collection. Screening of crystals is a typical task that can be (semi) automated, especially when a robot is used.

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Automated data collection

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  1. Automated data collection Peter ZwartBerkeley Center for Structural BiologyPhysical Biosciences Division, LBL

  2. Automated data collection • Screening of crystals is a typical task that can be (semi) automated, especially when a robot is used. • The benefits of automated screening primarily lie in • Efficiency in screening • Reduction of human errors in repetitive tasks • Tracking the results • DCS already had/has quite a number of sophisticated tools that allow HTP screening and collection • It however lacks fully automated analyses of images and has other drawbacks • The WebIce server allows an automated characterization of X-ray images via an analyses done with the Labelit suite (indexing, automated image quality, point group assignment)

  3. Automated data collection As part of a major BOS upgrade, Nick Sauter, Yun Zhou, John Taylor, Paul Adams and myself have been working on implementing automated screening and data collection facilities in BOS. Key ingredients: A data base that holds user provided sample information (which crystals in which puck in which position) An external server providing data analyses Indexing, diffraction quality, resolution estimates, data collection strategy Automated crystal centering software (XREC) BOS Gyorgy Snell & Josh Stillwell

  4. Screening & Data collection Sample information (Xtal ID, Puck name, Position in Puck) Samples in dewar Generate new run list Samples in run list Mount next pin Analyze data WebIce, manual (auto) center All done? Take snapshots ? Collect / Continue Unmount pin

  5. Automated crystal centering XREC is used for automated crystal centering It works well on 5.0.1 5.0.3 has some lighting issues that need to be addressed Auto centering is a two stage procedure Finding and centering the loop in low mag Finding and centering the crystal in the loop in high mag An iterative approach is used and is relatively robust Automated centering usually takes less than 90 seconds Manual centering is still faster though

  6. The new interface Center/Robot Tab Maps puck name to robot dewar position Familiar centering interface Log window: Shows all what happens A ‘light’ version of the logfile (with mounting, unmounting etc info) will be available in the near future A scoring tab allows efficient manual classification of diffraction quality

  7. The new interface TasqQueue Tab The interface between the database and the BOS user Search for puck names and add the crystals / pucks to the Queue Decide in which SIL (Sample Information List) you want WebIce to store the results of the analyses Start the data collection by pressing START

  8. The new interface After starting the Queue, crystals will be mounted User will center crystal or XREC will run 0 and 90 snaps are taken (and xtal jpegs are saved) Images fed to WebIce for analyses Current crystal is unmounted, next crystal is mounted Etc etc etc The WebIce tab in BOS shows the results of auto indexing, resolution estimates and gives an overall score to the two images The system works reliable I have used it to screen about 6 pucks of real crystals myself From my sofa

  9. The new interface After starting the Queue, crystals will be mounted User will center crystal or XREC will run 0 and 90 snaps are taken (and xtal jpegs are saved) Images fed to WebIce for analyses Current crystal is unmounted, next crystal is mounted Etc etc etc The WebIce tab in BOS shows the results of auto indexing, resolution estimates and gives an overall score to the two images The system works reliable I have used it to screen about 6 pucks of real crystals myself From my sofa

  10. WebIce WebIce allows you to view the snapshots the results of the analyses From any where as long as you have an account Your LDAP name and Password Data are grouped in SIL’s

  11. Communicating with the data base How to populate the data base with your data? Manual entry Spreadsheet upload (under development) Other External application Extracting information from the data base External application Spreadsheet download Issues Spread sheet uniformity / standards

  12. Conclusions & Acknowledgements Automation efforts in BOS are in a stage close to beta testing Acknowledgements John Taylor Yun Zhou Nick Sauter Paul Adams Ana Gonzalez Boom Moorhouse Gyorgy Snell Josh Stillwell

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