Known glitches

Quick jump to selected sections:

8. SerialEM crashes.

10. DM (GMS) crashes.

11. K3 lost part of the view, e.g. blank horizontal slabs.

1. On the K3 server, Programs appear frozen when deleting files from X: drive

what to do: It takes up a lot of I/O resources when freeing up space on X:drive. You need to stop tasks involving I/O, including data collection, before deleting a large amount of  data from X:drive (permenent deletion or empty recycle bin). Be patient, to free up ~2 TB space, the system may appear frozen for ten minutes, so it’s recommended you clean up files in small chuncks (up to 1 TB at a time). If you try to remove more than 5TB at once, it may appear frozen for over 30 minutes. It will come back to life eventually. Do not start new tasks when the system I/O is busy.  

2. GIF full tune exits early.

what to do: Restart Gci2Remote and GfiRemote and try again. Shortcuts can be found on the desktop. Alternatively, you may select the unfinished steps in Quick Tune and run them individually. 

3. GMS disapeared from the windows taskbar at the bottom. SerialEM main window is not visible.

what to do: use Alt+Tab to find it. Do not start another GMS without checking the windows task manager.

4. SerialEM COM error getting image from Camera; DM Aquisition Error: Capture time out!

This may be caused by busy I/O actions, including but not limited to copy/move/delete data, upload/download data during high-throughput data collection.  

what to do: Confirm the error message in SerialEM, Stop data collection;  check the message in the DM output area. Save screenshots of both. If either SerialEM or DM crashes, follow the proper procedures to recover them. Verify column valves status. After a certain period time of idling, the valves may be closed by SerialEM. Open the valves if necessary using the Open valves button in SerialEM or by clicking the Valve in DM.  Do a test shot in DM and in SerialEM to confirm the system can take pictures. Stop any heavy I/O operations, or wait for them to finish. Resume data collection. 

5. ZLP centering routine cannot find the peak (mask image is distorted).

what to do: First check the beam is visible by taking a picture; then verify the primary energy under filter control pallette is 300kV, if not, mannually change it to 300kV. Select ‘Mask’ aperture under Filter control, take an image, if the array of holes is aligned well, proceed to try ZLP centering again. If the array of holes is severely distorted, open a previously saved gdf file under Gatan/Prefs, verify the mask image is restored to normal, then re-do GIF tuning. Sometimes it also requires you to restart DM (follow the proper procedures). Since restarting DM takes a long time, only try it when the procedure described above doesn’t help upon multiple attempts.  

6. Linear mode not visible in TEM imaging.

what to do: Go to Help -> User mode, select Power user; Click the home icon of the Techniques pallette; Click TEM imaging.

7.  In the user interface, autoloader vacuum is off and autoloader becomes uninitialized. Autoloader reports docking/undocking failure.

If this happens before inserting the nanocab, the green button will not light up when the nanocab is inserted.

what to do: click Vacuum On in the autoloader flap-out menu, then click Initialize when the button is clickable. Resume operation if it returns to normal. Otherwise, cease operation and report to the staff or Thermo customer service.

8. SerialEM crashes unexpectedly.

what to do: check DM information area (near bottom), to see if there is any error message –> capture a test image in DM, confirm DM is operating normally. Restart DM if necessary (run Tune GIF or Center ZLP after DM restarts ) –> restart SerialEM –> Open column valves (yellow button) if the valves are closed upon crash –> load your customized setting file, read and open the navigator file –> activate low dose mode and check each low dose mode (Record->Focus->View. Important: must follow this order!) -> double check all the camera setup parameters, modify the image saving number if necessary –> resume acquisition.

9. SerialEM pops up stage error; the user can’t move stage using the navigator.

what to do: first, check if you can move stage in Titan UI, including using the joystick on the control pads. If stage movement is normal in the Titan UI, then simply restart SerialEM. If Titan UI reports stage error too, then report to the staff or Thermo customer service. If no error is visible, check Stage2 -> flap out menu -> Settings, to see if the Enabled button is yellow, the normal color. If the color is not yellow and is orange or grey, try to click it to disable it, then click it again to Re-Enable the stage. The process of Enable takes about six minutes and the button should return to yellow if it completes successfully. After the stage is re-enabled, the coordinates in the old navigator may become invalid, try to re-align a marker (shift to marker operation) between the atlas/Search mag (~175x) and View mag (~2250x). 

10. DM (GMS 3) crashes.

what to do: First, re-familiarize yourself with the Titan operational guide.

Verify there is no active DigitalMicrograph process in windows Task manager, force end it before restarting DM. -> Start DM/GMS 3 (click OK/Yes in the two popup warnings, the first says ‘…elevated previleges…’, the second says ‘…incompatible plug-in’ -> verify temperature under Camera Monitor, it should be -20C -> Go to Help -> User mode, select Power user -> Window menu/floating windows, click filter control ->  Click the home icon of the Techniques pallette; Click TEM imaging. -> Camera menu -> insert camera (takes up to one minute), pay attention to the Vacuum value of the Projection (CCGp) and make a note on how high it spikes. -> In filter control pallette, open a previously saved gdf file (GIF setting file) under Gatan/Prefs -> Go to an empty area,  center ZLP following the proper procedure. 

11. K3 lost part of the view, e.g. blank horizontal slabs, due to bad sync.

what to do: DM’s Camera monitor -> settings gear -> quick scan -> reset datalink -> click OK and re-scan until lights are all green (may need to repeat the reset a few times) -> return to normal interface -> take a shot in DM to see if it is recovered -> if the lost part remains, update dark reference in DM and try again. Check the gain reference image itself to see if it shows obvious slab artefacts, if so, then gain needs to be redone. If the problem persists after multiple attempts, restart DM (follow the proper procedure in #10 above) and/or recollect the counted gain reference (skip the linear gain reference). 

12. K3 does not auto-retract after the set time.

what to do: Retract it manually. Since the K3 cannot retract automatically after idling, it’s recommended that the user manually retract it until this software bug is sorted out in the future. Besides manually selecting Retract, the following actions trigger K3 retraction too: DM is closed; TEM UI is closed. 

13. DM pops up warning when you try to open a DM4 file by double clicking the file within windows explorer.

what to do: Do not double click it, use File -> Open to select the file.

14. After inserting phase plate, the beam on the fluscreen develops a halo.

what to do: Check if the phase plate heater is off. If so, turn it on. Unfortunately, the phase plate won’t function properly immediately after the heater is switched on. It takes a few days to stabilize. The phase plate heater power supply is mounted at the top of the microscope instrument cabinet. 

15. Capture timeout.

SerialEM is stuck at Record, no error per se, but does not procceed to the next step for several miniutes or longer. Sometimes it will proceed eventually without intervention, and other times it throws timeout error. DM’s output window shows capture timeout.

what to do: press Stop/END all in SerialEM, until the process is completely stopped. Make sure no other tasks are occupying the computer resource, such as transferring data or deleting data. If neither SerialEM nor DM crashes, verify DM can take pictures (View or Capture), verify SerialEM can take pictures (View or Preview), then resume the data collection. If either one crashes, then follow the proper procedures to recover them.  

16. Unload/Load cassette failed: The operation failed.

what to do: check the nanocab to see if the cassette is physically undocked or docked. If the physical state matches the operation, click Vacuum On in Autoloader OCX-flapout tab, wait for Vacuum On to turn yellow, then click Initialize. If these manual recovery is successful, resume normal operation. Otherwise,  cease operation and report to the staff or Thermo customer service.

17. DM reports ‘Images of different size cannot appear in the same expression’ during GIF tuning.

what to do: restart DM following the proper procedure. 

18. TEM server crashes as “BrickBox application process ‘Tem’ ended unexpectedly”. Such crashes usually cause High Tension to turn off and Autoloader to become uninitialized.

what to do: report to staff. Authorized users may perform the fix involving restarting the Tem Server.

19. Upon docking/undocking cassette, it reports ‘Unload cassette failed’. Autoloader can’t be re-initialized. 

what to do: check the nanocab, to see if the docking/undocking task is actually completed, if not, cease operation and report to staff/thermofisher. A protective clip of the communication cable is missing at the moment, which may cause the cartridge gripper connector to fall off. This bracket is on order and to be installed in the future. 

20. Autoloader error: Load/Unload cartridge failed. The stage is not available.

what to do: move the stage using joystick and click on the stage2 grid map in the UI, to confirm if the stage is functional. If it can be moved by joystick and UI, this error is false. Try Unload the cartridge again. If the stage can’t be moved by joystick, then there may be a real malfunction of the stage. Troubleshoot stage or report to staff/Thermofisher. 

21. Gain reference collection exits after the linear part, without doing the counted part.

what to do: make sure to select ‘Counted’ under TEM imaging, and try again. Alternatively, open the camera menu from the menu bar -> press and hold Alt -> click ‘Prepare Gain Reference’ under the camera menu -> select counted mode.

22. DM pops up window ‘Gatan USB Serial Communication: USB serial communication on COM 3 failed. Please check the USB cable connection, then press ‘Retry’ to try again’.

what to do: First, check if the data collection by SerialEM is running normally. If so, then ignore the window by moving it to the corner of the screen. This error may prevent DM/SerialEM from changing slit width and apertures, which will make Center ZLP fail. Clicking Retry may restore the function. If data collection stops and can’t be restarted, then end DM in taskmanager and restart DM following the proper procedure.

23. After system reset (e.g. Upon Titan UI crash, Tem server crash, Titan PC reboot, and other software and hardware issues on the microscope side.), the beam intensity or diameter appears very different from before under the same settings.

what to do: use the ruler to measure the beam size and compare it with the nominal illuminated area. Do this for both nano probe and micro probe. Write notes on their discrepencies. First, load a supervisor/customer service alignment from ‘Alignments’ OCX. Sort it by Date&time, select the latest one and apply. Go to ‘FEG Registers’ OCX, Sort it by Date, select the latest one and press Set. This should fix the discrepency issues. Double check the beam diameter and dose rate, confirm they are restored. 

24. Camera Time out error in SerialEM, Blankershutter monitor shows EFCCD is offline (red).

what to do: go to Titan UI/Camera panel, Select EF-CCD in the drop-down menu, try clicking ‘To online’ button (red) to see if it fixes the problem. If not, close TIA (Titan PC) and DM (Gatan PC), restart DM, then TIA. Follow the proper DM recovery procedures. 

25. DigitalMicrograph hangs when loading ‘EMcontrol’ during startup.

what to do: kill DM in taskmanager, remove ‘C:\ProgramData\Gatan\Plugins\ThermoScientificTEMPlugin.dll’ temporarily. Try starting DM again. If it starts up normally, close it, restore ThermoScientificTEMPlugin.dll to the original folder, try to start DM again.

26. Can’t select linear mode in DM.

what to do: restart DM following the proper procedure (see #10).

27. In SerialEM, square montage using View shot covers a much smaller area than it should be.

what to do: check montage setup, to see if the Total area in microns is the right size. Close the old montage file (File -> Close), set up a new montage and try again.