Contents

• List of Tables
• List of Figures
• User Information
  • STXM Principle and Overview
    • STXM Principle
    • STXM 5 Coordinate System
    • Scan Devices
    • Detectors
      • Outboard Detectors
      • Inboard Detectors
  • Running STXM V: The Essentials
    • Overview
    • Brief SM_GUI Overview
    • Using the Visible Light Microscope (VLM)
    • Exchanging specimens
    • Changing specimen mounts (e.g., wet cell)
    • Taking Scans
    • Moving the Sample and other Scan Devices
    • How to find and record the X-ray focus
    • Changing the photon energy
    • Acquiring point spectra
      • Recording defocused point spectra
    • Acquisition of spectromicroscopy ``stacks''
      • Short and Simple
      • In Detail
  • Running STXM V: Inboard Particularities
    • Taking Care of the Segmented Silicon Detector
    • Filling the chamber with helium
    • Venting from helium to atmosphere
    • Using the helium flow system
  • Wet Cell
  • The SM_GUI Graphical User Interface
    • Starting SM_GUI
      • Starting SM_GUI in a licensed IDL session
      • Starting the precompiled version on the Virtual Machine
    • More options to choose the program mode
    • GUI overview
    • The Draw Windows
    • Display Parameters Area
      • The Histogram Display
    • Spectra Settings Area
    • Signal Type, Detector and Display Area
    • The Display Information Area
      • Marking rectangles in an image
      • Fitting spectral peaks
      • The "Move Scan Devices to Mouse" button
      • The "Recenter Piezos" button
    • The Microscope Control Area
      • Shutter Control
      • Beamline Control
      • Silicon Detector -- Calibrate Now
    • The File Menu
      • Opening and Saving Data Files
      • Data Export
      • Printing
      • Additional Entries
    • The Alignment Menu
    • The Scan Menu
    • The Move Menu
    • The Extra Menu
      • Change Colortable
      • Use Nearest Neighbor Sampling on Zoom (no Interpolation)
      • Display Crosshair on Mouseclick Position
      • Plot Noise per Line in iTool
      • Image Processing
      • Edit Pointlist
      • Statistics
      • Zoom In, Zoom Out
      • Set up Stack
      • Start Stack
      • STXM 4 Display Settings File
      • Re-read Config File
      • APS File Read Settings
    • The Advanced Menu
      • Use Laser Positions
      • Homing
      • Track ZSTG in Spectra
      • Adjust Feedback Parameters
      • Monitor ADC Signal
      • Calibrate SGM
    • The Help Menu
    • The Toolbar
    • STXM 4 Support
    • APS Data File Support
      • Restrictions
      • Availability of Signal Types and Meaning of Data Values
      • APS File Read Settings
    • The SM_GUI config file
  • Running STXM V: Problems and Frequently Asked Questions (FAQ)
    • Help! I can't see my sample, the image is all black! (Or white)
    • Help! What's the difference between opening / saving data files files on the server and locally?
    • Help! I want to take a scan, but I have only one scan type to choose from in the scan menu!
    • Help! How can I print directly to the printer on Unix machines, rather than to a file?
    • Help! My scans on the inboard STXM look very noisy!
    • The scanning program (sm_gui) can't connect at startup
      • sm_server has crashed
      • Another client is connected
      • Your connection settings are wrong
    • The scanning program (sm_gui) get's stuck at startup
    • How do I remount the data folder?
    • What to do if the computer window seems locked up
    • Rebooting the computers
      • Rebooting the client computer (Linux)
      • Rebooting the server computer (Windows)
    • Beamline EPICS motors: x1a_mot_server
    • Beamline printer problems
    • After a crash
  
  
• Advanced information
  • The Scan Process in more Detail
    • Scan Types in the Scan Menu
    • The Scan Setup Window
      • Detector channels to record
    • The Scan Process
    • Scanning the Monochromator (EV)
      • Scan Direction
      • Linearity in Monochromator Scans
    • Scan Directions and the Orientation of the Image
  • Obtaining Data Files for later Analysis
    • File Naming Conventions
    • Downloading Data Files from the Web
    • Burning Data Files to CD / DVD
    • Accessing Recent Data Files
      • Directly in the microscope control program
      • From the thumbnail website
      • From the file system in the X1A network
  • Which Data STXM 5 Records -- STXM 5 Display Concept
    • The 3-dimensional Dataset
      • Which Signals are read by Default
    • Signal Types ("Flavors")
      • Raw Integers (image_data_intraw)
      • Raw Counts / mVolts (image_data_raw)
      • Calibrated kHz (image_data_khz)
      • Predefined Combinations
      • Custom (User-defined) Display Combinations in SM_GUI
    • Choosing Different Signals in SM_GUI and read_stxm5.pro
      • Choosing the Display in SM_GUI
      • Choosing the Display in read_stxm5.pro
    • Predefined Combinations
  • Reading and Understanding STXM 5 Data Files
    • The Contents of STXM 5 Data Files
    • Viewing Data Files in SM_GUI
    • Reading Data Files on the IDL Command Line
      • Reading Point Spectra
    • The sm_par Structure
    • Writing STXM 5 Data files with write_stxm5.pro
    • Changing / Overwriting Data Files
    • Silicon Detector Calibration
      • Calibration Model
      • Calibrating the Detector
    • The Structure of the netCDF File
    • Data File Format Changelog
  • Client-Server Concept and Networking How-To
    • Client-Server Concept
    • X1A and NSLS/BNL Network Structure
    • Microscope Remote Control
      • x1a subnet
      • BNL intranet
      • Outside world
      • Tunnelling the VLM
    • Access to Data Files "Locally" and "On the Server"
  • Alignment of STXM V
    • Homing of stepping motor stages
    • Initial alignment
      • Visible light microscope (VLM) setup
      • Detector prealignment
      • Beam into the chamber
      • Aligning microscope components
    • Correcting the tilt of the ZSTG axis with respect to the beam axis
      • Determining the drift parameters
      • Software correction
      • Hardware correction
    • Aligning the laser interferometer
      • Aligning the mirrors
      • Adjusting the receiver gain
    • Aligning inboard STXM to the Nitrogen edge
    • Mounting of ZP and/or OSA on glass cones
  • Configuration and alignment files
    • The alignment file
    • The configuration file
    • The silicon detector calibration file
    • The beamline slitsettings file
    • The NSLS ring parameters file
  • Moving Motors with the XPS Controller
    • Web Interface
    • Remote Control
  
  
• Bibliography