Argonne National Laboratory


User Program

Department of Energy Office of Science
GM/CA @ APS Sponsors:
National Institute of General Medical Sciences (NIGMS) and National Cancer Institute (NCI) of the National Institutes of Health (NIH)

User Program - While at the Beamline - JBluIce - EPICS

GM/CA beamline control software is based on a combination of EPICS and a graphical user interface (GUI) conforming the look and feel of SSRL BluIce. EPICS is a toolkit for designing distributed control systems and BluIce is a control system for macromolecular crystallography beamlines popular due to its convenient all-in-one tabbed user interface. While initially the SSRL graphical frontend was deployed directly with a few changes due to differences in the layouts of beamlines, the underlying control system was fully designed from scratch with the purpose to rely on widely tested and supported EPICS hardware drivers. The GM/CA control system has less software layers than in the SSRL BluIce thus helping to easily access advanced features of hardware and implement faster beamline operations. Additional details of differences between the backends of GM/CA and SSRL control systems can be found here.

In the course of adding new capabilities to the system like the GUI controls for automatic diffraction and fluorescence rastering of crystals, automatic crystal screening and data collection along a vector, we faced a shortage of widgets in the Tcl/Tk programming language that had been the foundation of the SSRL BluIce graphical frontend. It pushed a transitioning the GUI to a more advanced Java platform that was initiated at the beginning of 2008. The process took 2.5 years and successfully accomplished in May of 2010 when all-new JBluIce emerged. To avoid any interruptions to the GM/CA @ APS operations during the transitional period, the software was operational in a mixed mode where new Java-based Tabs (Raster and Screening Tabs and later Collect Tab) were temporarily embedded into Tcl/Tk.

The JBluIce-EPICS software is an open source available for downloading from GM/CA @ APS files depository.

For JBluIce user manuals including some video tutorials see the GM/CA @ APS 'while at beamline' page.


The following JBluIce Tabs are currently functional:

On the Hutch Tab users can change energy, attenuate the beam, open/close shutter, control slits, position CCD detector and align the beam to the goniometer axis.

The Sample Tab provides the crystals view with two video cameras (on-axis microscope and a lower-resolution camera looking from a perpendicular direction) and the controls for sample illumination. It also offers diffraction images viewer, single-click selection of x-ray minibeam collimator, sample annealing, fine beam position adjustments and various other tools for sample environment.

The Screening Tab contains all the controls needed for screening crystals and their indexing with WebIce. This Tab also provides controls for the sample mounting robot.

The Raster Tab provides best-in-class controls for searching tiny optically invisible crystals and finding good spots on poorly diffracting crystals. Both diffraction and fluorescence modes are available. Rastering can be carried in fully automatic and user-managed modes. Polygon rastering can be selected to reduce the number of spots to be inspected with X-rays. The initial search area can be taken from optical loop centering. The data can be exported to data collection Tab for collecting partial data sets on multiple crystal spots.

On the Scan Tab users can acquire fluorescent spectra and perform fluorescence scans around chosen absorption edge in either automatic or advanced controls mode. The scans implement fast on-the-fly signal collection without stopping monochromator and automatic detection of the edge shift with respective shift of fine energy sampling range.

On the Collect tab users can do classic data collection operations such as composing frame collection sequences and viewing the acquired images.

Besides that, the Collect tab also offers vector data collection.

... and data collection strategy.

On the Analysis Tab users can preview the results of background data processing that is automatically spanned by JBluIce and runs on the beamline computing cluster.

The Log Tab offers controls for saving the parameters of the experiment.

JBluIce includes many automations that run behind the scenes including automated sample centering and scripts for automated beamline alignment after changing the energy between different absorption edges.

GM/CA @ APS is an Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Argonne National Laboratory

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