top of page

  1. Start the detector software

  • MobaXterm is a remote desktop application that allows you to remote into the Linux PC on which we run the detector software from the beamline control PC.

  • Open MobaXterm

  • Click on the session tab, and you will see a list of "Saved Sessions". Select the xspress login and open one tab

  • In this tab, scroll up or type the following:

    • Source exportZebra.sh

    • Zebra.sh

  • Click back on the session tab and select "xsp3" from the saved sessions. Open three tabs:

  • In the first tab scroll up or type:

    • Cd epics/bin

    • ./run_xspress3_7.sh

  • In the second tab scroll up or type:

    • Cd epics/bin

    • ./run_medm_7.sh

  • In the third tab scroll up or type:

    • python epicsrelay.py​

  • Some of these commands will open new graphical user interfaces that allow you to interact with the detector software. Users typically do not need to interact with these pieces of software. Staff members will use them to diagnose problems. Just minimize these- you can ignore them.

moba_icon.png
moba.png

MobaXterm Interface

Xspress3-edm.sh
xspress3.png
zebra-edm.sh
zebra.png
Start Software

​2. Open xmapGUI

  • Click on the icon on the desktop

  • Under the menu "Detector" at the top of the window, select "Run Zebra Reset Batch File"

  • Push the circle with a 1 and then hit start

  • If you get an error close and reopen and repeat and it should work

  • Set up ROIs (regions of interest) i.e. the elements you want to map.

  • NOTE: Elements for XAS have to be in the first 4 SCA.

  • Go to SCA -> Periodic Table Interface -> Click on element and emission lines of interest. This will populate the ROI Peaks list. Within this list, click on the elements you would like XANES on and select Toggle XAS. This will add these elements to the XAS Peaks list. Click Populate ROI, then close the Periodic Table Interface window.

  • When you set up the ROIs through the Periodic Table Interface, it will automatically apply the ROIs to all channels. If you modify any channels manually, remember to hit “Apply SCA to All”

  • Under SCA  Switch range.

  • Check all SCA’s.

 

xmapgui_icon.png

3. Open Master Data Queue

  • Click on the icon on the desktop

  • Note that the icon is called "Data Collect" even though the program when it is open says "Master Data Queue"

  • This program must be open for microscan and uXAS to run

  • In order for this program to be opened, the program ICS must be running and the stage software must be communicating with the program. These programs should be running properly, but if dataserver does not open, it is likely that one of these is the problem. See the trouble shooting page:

 

DataCollect_icon.png

 

4. Open the video software

  • Find the VNC icon on the bottom left side of the screen (pinned to the task bar) and open. This opens a remote connection to the computer running the video viewing software

  • When prompted for a password, enter bl23cam

  • Open a python3 window (bottom right on the task bar):​​​​​​​​​​​​

  • ​Type "python vidserver.py"

  • Open a second python3 window (you can right click on the icon and select open)

  • Type "python vidclient.py"

  • This opens a display of the videofeed. You can now close the remote connection.

  • On the main PC, open a cmd promt and also type python vidclient.py

  • A mirrored video feed should now appear with a label Receiving Video

python_window.png
VNC_toolbar.png
Location of VNC icon in taskbar
HutchPC.png
hutch_camera.png
hexapod.png

5. Open microscan 

  • A crosshair should automatically appear and the lowest zoom (F position) should be highlighted

  • Select the check box that says "show current region?"

 

6. Open uXAS

  • ​Under "detector file" drop down menu, select "Xsp_7ch.det". This should be selected by default.

 

7. PDU manager

  • This is a remote power strip for turning on and off the sample light and for power cycling certain instrumentation

 

8. Open the digital voltmeter (DVM)  

  • This is a remote power strip for turning on and off the sample light and for power cycling certain instrumentation (if needed while troubleshooting)

​​

9. Open HexGUI

  • Push poly1 or poly3 to get the optic of choice (or thru hole to get the through beam)

​

​10. Start the webcam

  • This allows you to see around the hutch

​​

11. Open remote desktop for access to the laser​​

  • This will show you the laser interferometer reading, which allows you to bring the sample into the focal point of the beam

microscan.png
uXAS.png
PDU.png
voltmeter.png

MicroScan

  • This software allows you to drive around your sample and drive in between different samples that are mounted on the sample wheel. Importantly, you also use this program to place your sample in the focal point of the beam.

  • ​​MicroScan allows you to select regions on your sample to map. You can select the area, step size (i.e. pixel size), energy, and dwell time (i.e. length of time spent measuring the signal in a single pixel). ​When you have focused your sample and selected your mapping region (and named your sample!!), you can send this information to the Master Data queue, which actually executes the mapping.

  • MicroScan does not need to be open to actually run micro-XRF maps; it is just a tool used to select the parameters for these maps.

Microscan_instructions.png
Software Guide Microscan

uXAS

  • This software helps you to set up a queue of micro-XANES spectra, which are then sent to Master Data Queue. Typically the actual selection of micro-XANES locations are selected using SMAK. The instructions for how to set up a queue using a combination of uXAS, SMAK and Master Data Queue are provided in the SMAK How-To:

​​

​​

  • ​​This software also allows you to move all motors, OTHER THAN the SAMPLE STAGE motors (driving around the sample stage is done using MicroScan 

  • The motor you most commonly move using uXAS is DETECTOR, which moves the detector in and away from the sample

  • Importantly, this software also allows you to run "macros" that your beamline scientist sets up to enable you to switch energies and optimize beam intensity

uXAS_instructions.png
uXAS_run_macro.png
uXAS

Master Data Queue

  • This software runs all your scans- maps, XANES, etc. It MUST be open in order for MicroScan GUI and uXAS to open. 

MasterDataQueue_instructions.png
Create_button_instructions.png
DataQueue

Hexapod GUI

  • This software allows you to select the optic. The buttons listed are the ONLY ones you should touch.

hexapod_instructions.png
Hexapod GUI

BEAMLINE OPTIMIZATION

 

These instructions tell you how to optimize flux at the beamline and how to calibrate the monochromator. The beamline scientist will have already done this for you when you arrive for your beamtime. You may want to do this yourself, but only proceed if you are an advanced user.

​

Optimize flux at beamline​

  1. Move to the desired energy. In uXAS click “Move MONO”. Enter desired beam energy and click “Move”. Wait for mono to finish moving and click “Done”

  2. Optimize THOR and TABLE positions to optimize beam flux:

  • Under the "run" menu in uXAS and then select "custom scan". A new window will appear. Select "Ext_Scan_THTAB_3x" and hit ok.

  • This will scan the table vertically and horizontally to center the experiment on the beam maximum. These scans will be done in triplicate. This happens automatically, simply wait until the small box that pops up (which enables you to abort) dissappears.

 

A note on the focus of the optics when using macros to move to different energies

  • The beam focus changes with TUNE. The macros used to move between different energies typically use TUNE, then you need to load an optics_config file for that energy. Your beamline scientist will have made this for you and told you what it is called.

  • To open a specific optics_config file, in HexGUI select “Load Config File”, then select the optics_config file that you were instructed to use by your beamline scientist (Do NOT use other optics_config files. These could be out of date and would lead to unfocused optics).

 

Calibrate MONO

  • Remember that foils that are designed for energy calibration MUST BE MEASURED IN TRANSMISSION. If you cannot measure in transmission and must use fluorescence, use the foils that are prepared for concentration calibration

  • Place foil in front of I1 (using the foil on the sample wheel)

    • Use macro in data queue OR uXAS to move to appropriate Foil

    • If, instead of using the foil wheel, you put the calibration foil on the sample holder drive to the calibration material and focus on material by toggling red arrows in Microscan GUI until the laser reads zero

  • Open “Scan Motor” window in uXAS. Move MONO to the position of the absorption edge for the element of interest, e.g. 7112 eV for Fe

  • Scan I1 versus MONO from -10 to 10 (relative) in 0.3 eV steps. You can count for either 0.5 or 1 s.

  • When the scan is complete, hit “derivative”

  • Select the maximum of the derivative and hit “Move”

  • In microXAS GUI, go to Configure > Calibrate MONO.

  • In “Move to” you will be at the current position of the maximum of the derivative.

  • In “Calibration” enter the calculated value of the absorption edge for the foil (e.g. 7112 eV for Fe).

  • Click “Done”.

  • Click “OK” to recalibration message.

  • This will correctly calibrate the MONO for multienergy mapping, which will be different than for XANES.

  • Check the calibration for XANES by running a XANES scan – name the file “XX_foil”.

  • Check the position of the first maximum of the first derivative. DO NOT recalibrate the MONO, just keep this file for data processing.

​

Beamline optimization
bottom of page