Multi-D Acquisition window freezes when changing window size

[caichangjia]

Hi, I am using micromanager2.0 for Andor Zyla 5.5 camera on a Win 10 machine. I could run the following lines to capture a multi-D stack with full FOV size. However, when I switched to a smaller window size, the acquisition window will freeze and no output (see attached image).
If I capture with Multi-D Acquisition GUI (instead of code) and the issue is not there. Let me know if I missed anything, thank you!

core = Core()
TriggerMode = ['External', 'Internal (Recommended for fast acquisitions)'][1]
AcquisitionWindow = ['Full Image', '1024x1024', ' 512x512', ' 128x128'][3]
ElectronicShutteringMode = ['Global', 'Rolling'][0]
Overlap = ['On', 'Off'][0]
Exposure = 1.5

properties = {'TriggerMode': TriggerMode, 'AcquisitionWindow': AcquisitionWindow, 
              'ElectronicShutteringMode': ElectronicShutteringMode, 'Exposure': Exposure, 
              'Overlap': Overlap}#, 'FrameRate': FrameRate}
for key, value in properties.items():
    core.set_property('Andor sCMOS Camera', key, value)

save_name = r'acquisition_small_movie'
with Acquisition(directory=save_dir, name=save_name, ) as acq:
    events = multi_d_acquisition_events(num_time_points=400, time_interval_s=0)
    acq.acquire(events)

[marktsuchida]

What exactly do you mean by "switched to a smaller window size"? Do you mean you resized the window with the mouse during (or after?) the acquisition?

@henrypinkard do you have any suggestions?

[caichangjia]

Hi thanks for your reply! I mean first do the acquisition with AcquisitionWindow = 'Full Image', then do another round of capture with AcquisitionWindow = 128x128 using the following code (I do not resize window with mouse):

with Acquisition(directory=save_dir, name=save_name, ) as acq:
    events = multi_d_acquisition_events(num_time_points=400, time_interval_s=0)
    acq.acquire(events)

Hope that clarifies a bit.

[marktsuchida]

Ah, I see. So the problem occurs when the cameras ROI is set using the AcquisitionWindow property.

It might be worth seeing if it make any difference if you set the ROI using core.set_roi(x, y, width, height) instead.

Also, does the problem only occur when an acquisition with a larger ROI was previously run? Does it make a difference if you first run with a small ROI and then switch to full sensor?

It would probably help to know your exact Micro-Manager (nightly) and pycro-manager versions, too (if they are not both the latest, please try the latest).

[caichangjia]

Using core.set_roi still has the same problem. The problem happens every time when I change the ROI. But I could still do the multi-D Acq button in the GUI as normal. It just the command line no longer working. My mm version is MMSetup_64bit_2.0.1_20230619, pycromanager version 0.27.5

[marktsuchida]

@henrypinkard Would it be appropriate to move this issue to pycro-manager? Or NDViewer? Also any suggestions?

[henrypinkard]

I think you should try updating to the latest nightly build/pycromanager. This may be the same issue as https://github.com/micro-manager/pycro-manager/issues/620

[caichangjia]

Thank you. It is the same problem. My problem generally gets solved after updating to latest nightly build and pycromanager. However, there is still some small bug. After changing the size of the FOV (from 128x128 to full image) and use the multi-D acquisition using command line, the images are captured, but the gui still stuck there (same issue not happens when I use a small FOV like 128x128).

[henrypinkard]

Hmm I'm not sure. Are you able to reproduce this with the demo configuration? (I know you originally filed this issue on the main Micro-Manager repo, so it may be worth taking a look at the instructions for filing a good bug report on pycro-manager).

I'd be happy to take look into this more after you've gone through the procedure there, but I also need more information about the conditions for reproducing:

• Does it happen with the demo camera?
• What is the bit depth of pixels?
• what image sizes does it work for and which ones does it not?
• Which versions of pycro-manager, micro-manager, and which OS are you using?