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