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. 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 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

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 SILs

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