FastZ error that involved improper syncing with the NI PXIe and a possible “Machine Data File” error:

Make sure the connection to the NI PXIe is intact, and powercycle the NI PXIe and the computer.

If both the “GR mirror” and “Flipper mirror” controls are greyed out in ScanImage, it’s possible that Windows has assigned them the same COM port. To check, open the Windows device manager and look for the two entries called “Thorlabs flipper mirror” in the COM ports section. If they are both assigned to the same COM port, try the following: unplug the USB cables from both mirror control units, then unplug both power cables. After 10 sec, plug the power cables back in. Plug one of the USB cables back in and wait for the device to show up in the Windows device manager. Then, plug the other cable back in.

“Data logging lags acquisition by X frames”: This error occurs when the data storage folder is approaching its storage limit. Clean up some data and that solves the issue.

“COM port xx not available”: try restarting the computer and reopen scanimage. It is possibly some error of port assignment.

#

Berg4 Troubleshooting notes

Below are some troubleshooting notes detailing errors Elena and Habiba encountered when setting up Berg4 using ScanImage 2021.

• We were having issues with the X galvo feedback being off from the command signal when looking at the calibration in unidirectional scan. This was due to having a zoom factor of 1 and fast acquisition settings which were not within a range that one would expect to image under and were too fast for the galvo to keep up with. Increasing the zoom factor resolved this and we never had any problems with it during actual imaging sessions.
• Orange warnings upon scanImage startup referencing “enable” or “FastZ” were due to using .usr files from older scanImage versions (2020) in scanImage 2021
• TOC errors (when switching between modes) seemed to be a result of a change in Matlab’s timer callback function (used in the DelayEventListener scanimage file) introduced in Matlab 2021b. As of 10/27/21 ScanImage supports Matlab2021a and lower versions.
• We were having trouble rotating the mirror using the main GUI (but not in the ROI manager). This was due to a bug where ScanImage assumed a certain mode configuration and did not check to update the scanMode based on the current mode. On 10/27/21, Mitchell from ScanImage added a SuportsROIRotation function in the RggScan file on line 679 to address this. You can find the modified file in https://github.com/wilson-lab/flyg/tree/master/scanimage/Modified_ScanImage_Functions
• According to Mitchell from ScanImage, it is expected behavior to be required to update optimization for the FastZ after changing stack parameters.