Automated data collection Peter Zwart Berkeley Center for Structural Biology Physical Biosciences Division, LBL.

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

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