Optogenetics module

The optogenetics module drives LEDs from the shared module board, for example to activate CsChrimson (the firmware is designed for 620–630 nm). For the motors of MODULE 3, build the motor part as for the sleep deprivation module.

MODULE	Outputs	Stimulator
3, mAGOLED	10 motors (odd channels) and 10 LEDs (even channels)	OptomotorSleepDepriver
4, LED	20 LEDs (all channels)	OptoSleepDepriver

Wiring the LEDs

Suitable red LEDs include the Cree C503B-RAN-CA0B0AA1 (RS 904-7367) and the Multicomp MCL053MD (Farnell 1581137).

LEDs connect to the same Darlington outputs as motors or valves. Each channel can sink up to 500 mA through the ULN2803 arrays, far more than an optogenetic LED needs.

• MODULE 3: wire the LEDs to the even channels, the V1–V10 connectors (channels 0, 2, …, 18). The motors use the odd channels, M1–M10.
• MODULE 4: all 20 connectors drive LEDs (channels 0–19); use both the M and the V connectors.

Each LED needs a current-limiting resistor chosen for its forward voltage and the current you want. Wire LED and resistor in series between the positive supply and the Darlington output. The intensity is set by this resistor, not by the firmware.

Channels and tubes

MODULE 3: OptomotorSleepDepriver

Each tube that is stimulated has a motor (odd channel) and an LED (even channel):

ROI	1	3	5	7	9	12	14	16	18	20
Motor channel	1	3	5	7	9	11	13	15	17	19
LED channel	0	2	4	6	8	10	12	14	16	18

MODULE 4: OptoSleepDepriver

Ten tubes, numbered as for the odour delivery module:

ROI	1	2	3	4	5	6	7	8	9	10
LED channel	0	10	2	12	4	14	6	16	8	18

LED commands

The firmware has two commands for a single LED channel (the full list is in the modules overview):

• P channel ms switches the LED on once: P 4 1000 lights channel 4 for one second.
• W channel on_ms off_ms cycles gives a pulse train: W 4 100 900 30 gives 30 cycles of 100 ms on and 900 ms off, 30 seconds in all at a 10% duty cycle.

Pulse trains suit protocols that need a given stimulation frequency, and avoid depolarisation block.

Stimulator settings

Choose the stimulator, with its settings, when you start tracking. Both are in ethoscope.stimulators.sleep_depriver_stimulators.

OptomotorSleepDepriver (MODULE 3) has three stimulus types (stimulus_type):

1. motor only: turns the motor (P on the odd channel);
2. LED pulse: one LED pulse (P on the even channel);
3. LED pulse train: repeated LED pulses (W on the even channel).

OptoSleepDepriver (MODULE 4) has two: 1, LED pulse, and 2, LED pulse train. It can also limit the number of stimuli given to each tube (number_of_stimuli, 0 for no limit).

Settings common to both:

Setting	Meaning	Default
velocity_correction_coef	Sensitivity of the inactivity detection	0.003
min_inactive_time	Seconds of inactivity before a stimulus	120
pulse_duration	Length of a single pulse, in ms	1000
pulse_on_ms, pulse_off_ms	On and off time of each cycle in a pulse train, in ms	100, 100
pulse_cycles	Number of cycles in a pulse train	5
stimulus_probability	Probability that a triggered stimulus is delivered	1.0
date_range	Time windows in which stimulation is active	none

Firmware

Load the module firmware with MODULE 3 for motors and LEDs or MODULE 4 for LEDs only, and PCBVERSION set for your board (10 for version 1.0, 11 for 1.1, 12 for 1.2 and 1.3).