Instructions | PhotometryBox

11
Connect optical and opto-electronic components
1. Connect "LED" BNCH ouptpus to LED drivers for channels 1 and 2
2. Connect "PD" BNC inputs to photodiodes for channels 1 and 2
3. Connect "Sync In" and "Sync Out" BNCs as required for specific experiment
12
Operation
1. Plug in power
2. Connect NI-DAQ USB-6009 to computer with USB
3. Open Strathclyde WinEDR software on computer
4. Navigate to Record-->Record to disk
5. Navigate to File-->New and set file name
6. You should see live traces on the screen but NOTHING IS BEING RECORDED YET
7. Set the "Power" switch to "on"
8. Set the "Record" switch to "off"
9. Set the "Osc" switch for each channel such that the oscillation is off
10. Turn the LEDs on one at a time using the LED driver and use the amplitude knob for each channel to set the light power for each channel
11. Flip the "Osc" switch for each cannel to start the oscillation
12. Set oscillation frequencies for each channel (I use 217 Hz for primary cannel and 319 Hz for secondary channel)
13. Connect the optical fiber to the mouse and preview the signal in the WinEDR software
14. Adjust light powers as necessary to obtain a raw signal and avoid saturation of raw fluorescence traces (channels 4 and 5)
15. Adjust the "Gain" for each channel so that preview signals (1 and 2) are non-zero and non-saturating. Note, "Gain" affects only the preview signals. I recommend calculating final signals post-hoc from the raw fluorescence traces and ignoring the preview signals.
16. Click "Record" on the StrathClyde WinEDR software. UNTIL THIS STEP, NO DATA IS BEING RECORDED
17. Start behavioral protocol and flip "Record" switch on the box to "on" to lock values in place and start "Sync Out" TTL pulses
18. Record session
19. Click "Stop" on StrathClyde WinEDR software. NOTE: Even after you stop recording, your data file will remain open and locked by WinEDR until you either close the program or open a new file. Do not start a new recording without creating a new file or you will risk over-writing your previous session.
20. Flip the "Record" switch to "off"
13
Post-hoc analysis
1. Unzip analysis scripts from "Post-hoc analysis scripts Matlab 20190426.zip"
2. Add scripts to Matlab path
3. Open the script fibPhotDemo.m
4. Set the frequency ranges for each channel by adjusting the variables params.freqRange1 and params.freqRange2 at the top of the script
5. Run the script and select the ".edr" file containing your photometry data
6. Processed data will be stored in three variables:
  dsTimes -- Time stamps for each data point in processed data
  dsVals1 & dsVals2 -- Processed data for channels 1 & 2
  syncInTimes & syncOutTimes -- Time of TTL pulses
7. Additional variables available
  rawVals1 & rawVals2 -- Data before photobleaching correction
  rawData -- Full data from ".edr" file

MarColnaghi wrote 01/20/2021 at 14:21

Hello there! I'm currently using the PhotometryBox for my experiment!

However, I'm struggling with the synchronization of the module with a behavioral camera.

It would be ideal for me to have the camera acquisition triggered by the SyncOut channel. Still, the TTLs that come from this channel have a fixed frequency (1second). Is there a way to modify the frequency?

Thanks for the good work and the incredible piece of hardware!

Best,

Marco

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sfowen wrote 04/26/2019 at 20:24

Matlab post-hoc analysis scripts have been updated to correct how the cut-off frequency for the final low-pass filtering of the processed data is determined

Are you sure? yes | no

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