Automated data collection

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
Take snapshots
All done?
?
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 SILs

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