Electron microscopy
Troubleshooting of Gatan Hardware and Software
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Troubleshooting of Gatan hardware and software can be very complicated and time-consuming, and often need Gatan on-site service if a severe or unknown issue happens. Some common issues and their solutions are:


i)     Problem: The DM (DigitalMicrograph) computer and DM get slower and slower after the PC is rebooted, for intance, as you use the microscope, change magnification and modes between TEM, STEM, Diffraction, GIF, etc.
       Reason: The Gatan driver(s) are corrupted.
       Solution: Deleting and reinstalling the driver(s) can fix the problem.

ii) Troubleshooting related to GIF software and hardware.

iii) Troubleshooting related to DigiScan.

iv) Cathodoluminescence system and their troubleshooting.


Some issues and their known solutions related to GMS 2.0.2 are summarized by Gatan as shown below [1]:

GMS 2.0.2 build 800 August 11, 2011

Issues Fixed in 2.0.2:
Found In
Number Version Summary
------- --------- ---------------------------------------------------------------------------------------------------------------------------
2228 1.9.3 References to the product/project GHIA in messages should be replaced
2398 2.0.0 "This program may not have been installed correctly" message maybe displayed on exit from LicenseInstaller
2923 2.0.1 ImageInfo.dll missing from 64-Bit install
2929 2.0.1 Cannot load a Prism DAC Cal and run an Energy Constant Calibration
2930 2.0.1 Quantum Prism DAC Calibrations deleted from GIB Settings
2939 2.0.1 Selecting the 'Insert' check box on the Camera View palette for an Orius SC200W produces an error message
2969 2.0.1 Maximum slit width not HT dependent
2971 2.0.0 LicenseInstaller may not copy files when other licenses were present
2986 2.0.1 Redefine idle mode for 1000XP and 1000XPFT cameras
3026 2.0.1 Calibrate Energy Constant does not work
3027 2.0.1 Import Prism Dac calibrations does not work
3028 2.0.1 Calibrate Spectrum Offset does not work
3029 2.0.1 Calibrate Drift Tube fine does not work
3030 2.0.1 Install GIF Measure Slit Currents returns incorrect values
3031 2.0.1 Using Control key to force tuning does not work
3032 2.0.1 Spectrum Tilt correction not working
3033 2.0.1 SX3 step size not configurable for user in spectrum tilt tuning
3034 2.0.1 Calibrate Condenser Adjust does not work
3056 2.0.2 Prism DAC Calibration does not work
3057 2.0.2 Lense step strength is not stored in FilterControlPlugIn
3058 2.0.2 Install GIF --> Spectrum and Install GIF --> Spectrum Binned do not work
3059 2.0.2 Cannot restart service level spectrum view using CTRL+R
3060 2.0.2 Mag tuning occasionally results in unexpected error dialog
3061 2.0.2 Tune ZLP from Install GIF Tune menu is slower than through AutoFilter UI
3062 2.0.2 Energy adjust always has a residual value after aligning ZLP
3063 2.0.2 Drift Tube continues to wobble even if the drift tube on checkbox is unchecked
3064 2.0.2 Position ZLP dialogs in FilterControlPlugIn are displayed behing the main application window
3116 2.0.2 'Tune High Order Aberrations' menu item is unnecessarily exposed for the 963 Quantum in Service mode
3160 2.0.1 DM crashes while loading camera for Enfina

GMS 2.0.1 build 697 March 28, 2011

Issues Fixed in 2.0.1:
Found In
Number Version Summary
------- --------- ---------------------------------------------------------------------------------------------------------------------------
467 1.6 Digiscan does not get the magnification value before each acquisition when running in continuous mode
1115 1.8.2 When resuming tomography on current angle, the angle set delay is used
1957 2.0.0 GMS setup wizard fails for case of x32 application with off-line x32 licenses in Win 7 x64 environment
2121 2.0.0 DMShellEx 64-Bit Registry entry does not match 32-Bit entry
2309 1.8.3 Mubar wrong for DigiScan preview
2319 2.0.0 Adding a custom integer data field to the Session Info data set causes a DM has stopped working error
2350 2.0.0 Calibration palette does not update when hit update status button
2352 2.0.0 When live view starts stage set to target. When live view dismissed stage set to target again -> another accidental kick to x,y
2360 2.0.0 Hideous "Orius Temperature Control not stabilized" dialog has no parent
2485 2.0.0 GatanScsiAssist service not running; as a result need Quantum or XP camera not found
2486 2.0.0 When GMS is deinstall, GatanScsiAssist service is not
2504 2.0.0 3D Visualization forced close
2512 2.0.0 Orius 831 & 832 Camera does not image in Quality mode & Fast Mode image is reversed
2514 2.0.0 ALT Key not allowed access to sub menu items to run scripts
2526 2.0.0 Live EELS Fourier deconvolution kills DM
2536 2.0.0 NLLS fitting gave continuous errors
2575 2.0.0 Runtime error received for the EDS Analysis Server during startup of DM x64 off-line configuration
2596 2.0.0 UltraScan XP Camera frame sequence tags are incorrect
2597 2.0.0 EDS Acquisition memory leak
2603 2.0.0 Dark Reference does not work
2608 2.0.0 RangeEELS vaporizes DM
2612 2.0.0 SEMControl Plugin loaded in off-line installation
2613 2.0.0 Drift tracking with selection does not continue
2614 2.0.0 Simulator EDS acquisition with fresh tags gives blank spectrum
2622 2.0.0 Minimum good exposure for tuning
2624 2.0.0 EFTEM-SI not set as EELS Data Set
2627 2.0.0 Images will be saved sometimes without their thumbnails
2645 2.0.0 AutoFilter dispersion text for ENFINA is disabled
2646 2.0.0 EELS Range not added by default for ENFINA
2653 2.0.0 In FiltercontrolPlugin, "Save As" behavior for the GIB Settings file is not intuitive
2657 1.9.3 EELS spectrum more intense in STEM-SI following artefact correction
2660 2.0.0 EELS processing live thickness measurement not working when show component is selected
2662 2.0.0 Compute Thickness does not update live ZLP when show component is selected
2663 2.0.0 ImageShift/BeamShift tracker addresses ImageShift only
2664 2.0.0 When stopping the Parent process the child processs stopped but the state still show a live process
2665 2.0.0 When applying Splice to Dual SI "Use sibling" option is not working
2667 2.0.0 SEMControlPlugin getting wrong microscope name
2668 2.0.0 SEMControlPlugin not loaded with Zeiss SEM
2669 2.0.0 Zeiss SEM doesn't realize it's a scanning microscope
2670 1.9.3 EELS line scan surveying does not update during acquisition
2671 2.0.0 GFA not installed with software suites or DigiScan
2677 2.0.0 Incorrect GFA installation instructions included in the documentation
2679 2.0.0 DM vaporises when ChromaCL extract color component is used on a non-RGB image
2688 2.0.0 Enter key does not work in edit field of script palettes
2689 2.0.0 TIF tags for Hitachi not written to TIF images
2692 2.0.0 SmartEBIC package does not acquire images
2693 2.0.0 SmartEBIC palette buttons stay in "pressed" state
2694 2.0.0 Microscope state never read from scope
2709 2.0.0 EFTEM-SI auto-exposure causes errors whan acquiring low to high
2715 2.0.0 Open image dialog defaults to DM4 (opening from Plugins only)
2716 2.0.0 Readout noise script at Bin x 4 fast mode does not complete
2717 2.0.0 Prepare Dark Reference from the Camera drop down menu causes camera timeout
2722 2.0.0 Installed EELS analysis User guide is way out of date
2729 2.0.0 unitialized variable breaks D4Y function on Enfinas
2730 2.0.0 Cannot display packed complex images larger than 2GB
2733 2.0.0 Live View in Diffraction Mode does not work
2735 2.0.0 64-bit DMSDK libraries missing
2736 1.9.3 During EFTEM SI acquisition from low energy to high energy the message 'This operation requires a tag list' is shown continually
2741 2.0.0 Initial pixel blanking not taken into account for hardware SI
2742 2.0.0 Order multi-map list hi/lo vaporizes DM if no item selected
2745 2.0.0 TEM Autotune has unsafe behavior on DM exit
2746 2.0.1 STEM Tomography does not start calibration wizard on missing stage orientation calibration
2748 2.0.0 Swtiching between EFTEM and EELS modes can yield 'Improper Argument' exception
2751 2.0.0 STEM Montage stage tracking is wrong
2754 2.0.1 STEMDetectorCalibration not installed with license for STEM Detector (806)
2757 2.0.1 Open SI palette causes DM to vaporize
2758 2.0.1 Field of View calibrations not seen by calibration software
2760 2.0.1 EELS Exposure mode drop list on AF palette blank
2761 2.0.1 Setup button in EELS section of AF palette did nothing
2765 2.0.1 Stage calibration generates bogus suggested magnification
2766 2.0.1 Drift in first tilt step was not corrected
2772 2.0.0 Switching JEOL COM from STEM to Diffraction mode produces zero or incorrect Camera Length in DM
2780 2.0.0 PVCAM_CameraPlug-in.dll does not load error received when connected to & licensed for the ES500W camera
2781 2.0.1 Continuous view appears to be cumulative
2782 2.0.0 TEM AutoTune does not work on CM microscope
2789 2.0.1 Montage not waiting for stabilization delay on image shift between images
2794 2.0.1 Stage shifts in opposite Y direction to that expected by Montage
2796 1.9.3 Overlaid EELS edges plus background vaporises DM
2801 1.9.0 Import planes does not work
2802 2.0.0 Montage setup deadlocks DM when using an overlap of 0%
2803 2.0.1 Cannot build core scripts using existing install.s, complains of invalid package level
2804 2.0.1 STEM Tomography xy tracking fails
2805 2.0.1 STEM Montage uses tomography zoom factor after a tomography run
2808 2.0.1 Factory Configurations folder missing .des files
2822 2.0.0 missing functionality: no way to set Quantum lens card name in filtercontrolplugin
2824 2.0.0 Digiscan signal settings for Offset and Gain are not being saved
2827 2.0.1 In an installation with both Enfina and ES500 1394 installed, the ES500 is not detected
2841 2.0.0 Image acquired through STEMUtilities corrupted after changing image size
2846 2.0.0 Coarse drifttube calibration broken
2847 2.0.0 IFC readprismadc function broken
2848 2.0.0 No way to import prism dac calibrations
2850 1.9.3 JEOL EDS components file not installed with EDSRemoteServer
2852 2.0.0 XuM Mechonics 32-Bit license is not recognized
2855 2.0.0 Mag and spot index mappings are broken
2857 2.0.1 Camera plugin throws error for gain corrected asymmetric binned acquire
2864 2.0.1 Lens Corrections computed but not applied during isochromaticity tuning
2866 2.0.1 "Install GIF:Calibrate Slit Currents" menu command broken
2869 2.0.1 Fine drifttube calibration broken
2876 2.0.0 3View Installer does not install files needed by stages
2912 2.0.1 prism dac calibration routine broken
2915 2.0.1 Camera tags stripped from prefs when STEMDetector plugin used

Known Issues:
(2861) .dm2, .dm3, .dm4, and .s file types are not associated with DigitalMicrograph in the 'off-line' license configuration
workaround: Manually associate the desired file type with the DigitalMicrograph executable.

1. In Windows Explorer, double click on on a file of the desired type (.dm2, .dm3, .dm4, or .s)
2. In the 'Windows cannot open this file' window, select the radio button 'Select the program from a list', then press the OK button
3. In the 'Open With' dialog, select the browse button
4. In the 'Open With...' dialog, focus should already be on 'Program Files'. double click on the 'Gatan' folder, then
select 'DigitalMicrograph.exe', and then press the Open button
5. 'DigitalMicrograph' should now be listed (& selected) in the list of programs on the 'Open With' dialog, check the 'Always
use the selected program to open this kind of file' checkbox, then press the OK button
6. DigitalMicrograph should launch and the file selected in step 1 should load.

repeat these steps to associate additional file types. DigitalMicrograph should already be in the list of programs
(possibly noted as the 'recommended program')

GMS 2.0.0 build 615 Feb 03, 2011

2.0.0 New Features:
* New FFT implementation, includes:
- no size restriction
- no dimension restriction
- no data type restriction
- packed complex format new for real8
- packed complex format for more than 2 dimensions
- much faster, uses all available processors/cores
* Packages and plug-ins can be created and loaded from a user’s individual plug-ins folder or the common user’s plug-ins folder in addition
to the traditional installed plug-ins folder
* new DM4 data format
- capable of saving files larger than 4GB
* Calibration Wizard to guide the user through microscope calibrations
* Montage, Tomography, and TEM Autotune automatically bring up a configured calibration wizard when they have unmet calibration needs
* Calibration palette completely redesigned
* Calibration configuration: e.g. do beam tilt calibration in imaging vs. diffraction mode
* New calibrations: objective focus calibration in Imaging mode, objective stigmation calibration (used in TEM Autotune)
* EFTEM microscope operating modes (added for FEI Tecnai/Titan microscopes)
* Support for the Hitachi H7700 microscope
* New improved STEM auto-focusing algorithm used in STEM Tomography
* Completely re-written; TEM Autotune is now integrated with other applications and more robust
* Redesign of 3View user interface, MFC based
* A new SEM Control palette
- provides easier access to Microscope from DM
- includes XuM navigation
- includes 3View stage
* XuM APT control is now a standalone palette
* Rework “advanced ColorCL palette” -- It is now GDI+ based (previously done with 3dr party ActiveX component)
* AutoFilter
- New AutoFilter interface for GIF and ENFINA users (upgrading from GMS 1.8)
- Much improved EELS acquisition UI
- Much improved EFTEM mapping UI
* EFTEM Mapping re-implemented
- Automated exposure and binning options
- “Multi-map” option for acquiring and storing multiple elemental maps in a single acquisition (requires Advanced EFTEM option)
- Advanced EFTEM-SI with auto-exposure and periodic table approach for extended EFTEM-SI acquisition (requires Advanced EFTEM option)
- Improved manual drift correction for 2/3 window EFTEM mapping
* EELS Acquisition
- Auto-exposure option
- Automated collection angle determination
- Cross-correlation during cumulative acquisition
- DualEELS support (requires supporting hardware)
- RangeEELS acquisition mode – acquire spliced EELS spectrum over extended energy loss ranges (requires Advanced EFTEM option)
* FilterControl
- Full embedding into DigitalMicrograph
* HAADF Control
- Added 807 support
- Added multi-detector support
* “Live” EELS analysis tools for actively processing live spectra during acquisition
* Faster GIF tuning, with GIF Settings Manager for managing microscope state-related tuning
* Support for GIF Quantum 963, 965, 966
* Added “differential” EDS acquisition for increased speed during EDS spectrum-image acquisition
* EDS spectrometer meta data embedded in spectra acquired from Bruker systems
* Savitsky-Golay smoothing filter added to Numerical Filters
* Added capability for voltage dependent gain references
* Added capability for voltage dependent energy constant calibrations
* Extended microscope operation mode list to include EFTEM modes

Issues Fixed in 2.0.0:
Found In
Number Version Summary
------- --------- ---------------------------------------------------------------------------------------------------------------------------
236 1.6.1 Font size of point annotations too small for large images
241 1.6.1 Microscope settings restored has screwed up microscopy settings
657 1.7.1 DigiScan causes abrupt program termination if large amount of memory is needed to acqurie images
664 1.7 Remove microscopeCOM dependency on vendor DLLs (TEMNetLG.dll for JEOL ARM1300)
751 1.7.1 IFC - First click only gets focus
780 1.8 Coolsnap EZ (Photometrics 1394 PVCAM camera) issues
839 1.8 On undocking the live filter setup palette window we lose all changed data
921 1.8 Microscope Calibration Dialog displays wrong items in TEM/STEM mode
938 1.8 Calibration state dialog issues
1066 1.8.2 ConeBeamReconstruction Error Messages Vague when Dongle Missing
1373 1.8.2 Start reconstruction button incorrect label after a failure due to lack of memory
1412 1.8.2 Installer sometimes comes up with extra camera ES500 in camera list
1425 1.9.0 DM crashes when DS controller is OFF
1511 1.8.3 Display of packed complex images is wrong
1515 1.8.3 SetPixel fails on packed complex images, and displays wrong error message
1561 1.8.3 DM crashes when using Line with length label tool in page view
1588 1.9.0 Closing live assisted alignment FFT window gives error
1590 1.9.0 Output of meaningless debug info to results window from Manual Stitching Algorithm
1638 1.8.2 License Generator does not have a 3 analog license
1727 1.8.4 DigiScan calibration incorrect when "Depends on magnification" checkbox selected
1765 1.8.2 STEM calibration scaling problem
1828 1.9.1 Error changing modes in fastTEM
1925 1.8.4 Confusing wording in Tracking setup dialog and menu
1935 1.8.4 Deinstalling GMS 1.8.4 destroys registry value "CommonFilesDir" in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion
1967 1.8.3 Calibration of DigiScan images works incorrectly
1983 1.8.2 Invalid calibration using CM_AcquireImage in diffn mode
2067 1.8.4 XuM Camera locks up
2104 1.8.3 check disc space before 3View record starts
2117 1.9.3 0s dwell in Digiscan Vaporizes DM
2175 1.9.3 DM crashes during startup when Tecnai Remote is not working
2207 1.9.3 Open text annotation causes crash
2256 1.9.3 Cooling monitor for camera does not handle -ve sign correctly leading to offset data
2263 1.9.3 Camera dark reference contains signal in frame transfer modes
2271 1.8.4 Changing tilt angles caused setup dialog to hang and require DM restart
2273 1.8.4 Saving of parameter sets seems to generate strange lists of parameters named "Default"
2427 1.9.3 DM Vaporizes when "Use Microscope External Control" is enabled
2429 1.8.3 Digiscan crashes on large images
2441 1.9.3 Incorrect ZLP model selected when Use Extract Zeroloss setting checked
2450 1.9.3 afgetcurrentviewcommand() Error in Results
2506 1.9.3 DM vaporises on startup if JEOL EMSetHighTensionOffset() fails
2557 1.9.3 Linearization does not work
2634 1.8.3 Batch Convert Browse button can vaporize DM
2666 1.9.3 Setting up new parameters sets with DSCreateParameters(...) overwrites old ones
2720 1.9.3 MLLS via script interface not working





[1] ftp://ftp.gatan.com/outgoing/DanielRay/ReleaseNotes.txt.