PyPhotometry 2 and Doric cube Gen3

[AtMostafa]

Hi everyone,

I'm setting up a photometry rig with the new pyPhotometry v.2 and Doric Gen3 in the 2EX_1EM_pulsed mode. I'm getting low SNR and trying to troubleshoot. Would really appreciate if anyone has any experience with the following questions:

• Is there a standard way to measure the LED power at the tip of the patch cord? Many papers recommend 30-50uW, is that to be measured in the continuous mode? In the 2EX_1EM_pulsed mode, there is no way I can get the power even close to that. Also, there are 2 wavelengths multiplexed, so the measurement can't be accurate, right?
• Do I have to remove any of the built-in filters in the Doric cube to increase the power, similar to the recommendations for Gen2 cubes?
• Is the latest release already compatible with v2 boards? I noticed some commits in the dev branch.

Many thanks and really appreciate any insight :)
Mostafa

[ThomasAkam]

Hi @AtMostafa ,

The Gen3 minicubes have neutral density filters in user accessible trays on the bottom of the cube which block 90% of the excitation light. For use with pyPhotometry you probably want to remove these filters, because pyPhotometry uses pulsed illumination which requires higher LED-on light intensities (though the average light intensity is low as the led is off most it the time).

To measure the light power at the fiber tip use the 2EX_2EM_continuous acquisition mode such that that LED is on continuously not pulsed.

You can use the current released version of the GUI with the gen3 minicubes but the actual led current will be 3x higher than shown in the GUI. The latest version in the dev branch let's you specify which board you are using and the led currents match the GUI values. The .ppd data format has changed in the dev branch version of the GUI, but the new version of the import_ppd function in data_import.py file in the dev branch handles both old and new ppd files.

Best,

Thomas

[AtMostafa]

Thanks Thomas for the prompt answer.

I'll remove the filters then. I assume it is fine to leave the space empty?! (apologies, I haven't seen the inside of these cubes).

[ThomasAkam]

Yes, the procedure for removing the ND filters should be detailed in the minicube manual, and you can leave the tray empty.