Stack pause no longer implemented?

AdvancedImagingUTSW commented 1 year ago

Trying to acquire a z stack on live cells rights now and the stack pause does not seem to work. Looking at feature and I don't see it as well.

zacsimile commented 1 year ago

What do you mean by stack pause?

AdvancedImagingUTSW commented 1 year ago

A wait time period between each time point.

zacsimile commented 1 year ago

Oh I don't think we ever implemented that.

AdvancedImagingUTSW commented 1 year ago

It's at least an easy addition. Imaging at nascar speeds on OPMv2 when I need school bus speeds.

annie-xd-wang commented 1 year ago

I can add it as an independent feature that can work with ZStackAcquisition.

AdvancedImagingUTSW commented 1 year ago

Okay, thank you. Essentially, if the user provides a stack pause, then that wait duration is introduced after each complete volume is acquired with all of the channels.

Thus in the perStack format: Channel 0, Time 0, all z positions Channel 1, Time 0, all z positions stack pause Channel 0, Time 1, all z positions Channel 1, Time 1, all z positions stack pause ...

perZ format Channel0, time 0, z0 Channel1, time 0, z0 Channel0, time 0, z1 Channel1, time 0, z1 Channel0, time 0, z... Channel1, time 0, z... stack pause Channel0, time 1, z0 Channel1, time 1, z0 Channel0, time 1, z1 Channel1, time 1, z1 Channel0, time 1, z... Channel1, time 1, z... stack pause ...

AdvancedImagingUTSW commented 1 year ago

And now that I think about it, this should be implemented in our 2d + t and confocal projection modes. Anything with multiple time points.

JinlongL commented 1 year ago

While testing out on the microscope, got the following error.

Exception in thread z-stack signal:
Traceback (most recent call last):
  File "C:\Users\Dean-Lab\miniconda3\envs\ASLM\lib\threading.py", line 973, in _bootstrap_inner
    self.run()
  File "C:\Users\Dean-Lab\miniconda3\envs\ASLM\lib\threading.py", line 910, in run
    self._target(*self._args, **self._kwargs)
  File "c:\users\dean-lab\documents\aslm\src\aslm\model\model.py", line 874, in run_acquisition
    self.snap_image()
  File "c:\users\dean-lab\documents\aslm\src\aslm\model\model.py", line 843, in snap_image
    self.active_microscope.daq.run_acquisition()
  File "c:\users\dean-lab\documents\aslm\src\aslm\model\devices\daq\daq_ni.py", line 231, in run_acquisition
    self.camera_trigger_task.start()
  File "C:\Users\Dean-Lab\miniconda3\envs\ASLM\lib\site-packages\nidaqmx\task.py", line 1026, in start
    check_for_error(error_code)
  File "C:\Users\Dean-Lab\miniconda3\envs\ASLM\lib\site-packages\nidaqmx\errors.py", line 127, in check_for_error
    raise DaqError(error_buffer.value.decode("utf-8"), error_code)
nidaqmx.errors.DaqError: Task specified is invalid or does not exist.
Status Code: -200088

Error codes can be found here

TheDeanLab / navigate

Stack pause no longer implemented? #398