Timer feature for recording start/stop?

[mccarthy-jm]

Hi,
I frequently do multi-hour overnight recordings, and would love to be able to set pyPhotometry to start/stop automatically to minimize photobleaching over the course of a multi-day experiment. Are there any plans to add a timer feature for starting and ending acquisition?
Thanks,
Jordan

[ThomasAkam]

Hi @mccarthy-jm,

This is a good idea but I don't think I am likely to have time to implement it in the near future. I have created an issue (#35) to keep a record of it. However there are some existing options that might enable you to achieve what you need in terms of tracking activity over long time periods while minimising photobleaching.

Firstly, could you reduce the sampling rate of the data acqusition? In the pulsed acqusition modes, each LED is only turned on for ~1ms each time a sample is aquired, so by reducing the sampling rate you proportionally reduce the average light intensity and hence photobleaching.

Second, it is possible to control the acqusition board directly from a python script without using the GUI, for an example of how to do this see acquisition_board_example.py. It should be pretty straightforward to modify this script to do sheduled recordings, e.g. recording 5 minutes every hour, and you could also plot the activity aquired in each run as the Acqusition_board.process_data method that is used in the script can return the signals for plotting.

[mccarthy-jm]

Thanks! I was able to use the example code to run timed recordings and it worked very well in combination with low light levels and a low sampling rate. One thing I wanted to point out in case anyone else is trying something similar - the example code seems to use the v1.1 file structure, but the board.start() command from before the synchronization pulse feature was added. For my purposes, I ended up editing my v1.0.2 installation to have the newer versions of the config files, but I think it would also work to edit the start command to say board.start(false) if you didn't want sync pulses?

[ThomasAkam]

Glad to hear you got this working. Your right that the acquisition board script had not been updated since the sync pulse output functionality was added so was not working. I've just pushed a fix for this so the version of the code in the main branch should now work correctly.