Hardware Setup¶

Detailed hardware assembly instructions for CLoPy experiments.

Parts List

Complete parts lists are available in the PDF: CLNF_Parts_List_and_Assembly_Instructions_Gupta_et_al.pdf

CLNF Hardware (Raspberry Pi)¶

Components¶

Component	Quantity	Notes
Raspberry Pi 4B+	1
Raspberry Pi Camera v2	1
MPR121 Capacitive Touch	1	Lick detection
LEDs (various)	4	Behavior, Reward, Fail, TTL
Water valve	1	Reward delivery
Speaker	1	Audio feedback
Power supply	1	5V 3A minimum

Pin Connections¶

GPIO Pinout (Board numbering)¶

┌─────────────────────────────────────────────┐
│              Raspberry Pi GPIO              │
├─────────────────────────────────────────────┤
│                                             │
│  3.3V  ──── VCC (MPR121)                    │
│  GND   ──── GND (MPR121, LEDs)              │
│  SCL   ──── SCL (MPR121)                    │
│  SDA   ──── SDA (MPR121)                    │
│                                             │
│  GPIO17 ──── Behavior LED (pin 1)           │
│  GPIO27 ──── Reward LED (pin 1)             │
│  GPIO12 ──── Fail LED (pin 1)               │
│  GPIO21 ──── Light TTL (pin 1)              │
│                                             │
└─────────────────────────────────────────────┘

LED Wiring¶

GPIO ──── Resistor (330Ω) ──── LED ──── GND

Water Valve¶

Connect to relay controlled by Arduino or GPIO.

Camera Setup¶

Connect camera to CSI port
Enable camera in raspi-config: bash sudo raspi-config → Interface Options → Camera → Enable
Test camera: bash raspistill -o test.jpg

I2C Setup for MPR121¶

Enable I2C: bash sudo raspi-config → Interface Options → I2C → Enable
Install tools: bash sudo apt-get install i2c-tools
Verify connection: bash sudo i2cdetect -y 1 Should show device at address 0x5a

CLMF Hardware (Jetson Orin)¶

Components¶

Component	Quantity	Notes
Nvidia Jetson Orin	1
Sentech Camera	1	USB3 preferred
Arduino Uno/Mega	1	TTL and LED control
Water valve	1	Reward delivery
Speaker	1	Audio feedback

Arduino Connections¶

Pinout¶

┌─────────────────────────────────────────────┐
│                 Arduino                     │
├─────────────────────────────────────────────┤
│                                             │
│  13  ──── Brain TTL (output)                │
│  7   ──── Reward LED                        │
│  12  ──── Fail LED                          │
│  40  ──── Light TTL                         │
│                                             │
│  GND  ──── GND (LEDs, TTL)                  │
│                                             │
│  Serial: /dev/ttyACM0                       │
│                                             │
└─────────────────────────────────────────────┘

Python Serial Configuration¶

board = Arduino("115200", port="/dev/ttyACM0")

Serial Port

The serial port may vary. Check with: bash ls /dev/ttyACM*

Camera Setup (Sentech)¶

Connect via USB3
Verify: bash v4l2-ctl --list-devices
Test capture: bash gst-launch-1.0 v4l2src ! videoconvert ! ximagesink

GPIO (Jetson)¶

Using RPi.GPIO library for compatibility:

import RPi.GPIO as GPIO

GPIO.setmode(GPIO.BOARD)
GPIO.setup(pin, GPIO.OUT, initial=GPIO.LOW)

Optical Setup¶

Microscopy Configuration¶

                    ┌──────────────┐
                    │   LED Array  │
                    │  (470nm for  │
                    │   GCaMP6f)   │
                    └──────┬───────┘
                           │
                           ▼
              ┌────────────────────────┐
              │    Filter Set          │
              │  (Excitation/Emission) │
              └───────────┬────────────┘
                          │
                          ▼
              ┌────────────────────────┐
              │    Camera              │
              │  (Pi Camera / Sentech) │
              └────────────────────────┘

Illumination¶

CLNF: 470nm LED for GCaMP6f excitation
Use appropriate filter sets for fluorescence imaging

Calibration¶

ppmm (Pixels per mm):
Image a ruler at your optical magnification
Count pixels across known distance
Set in config: ppmm = <count>
Bregma Location:
Image the skull landmarks
Note the (row, col) coordinates
Set in config: bregma = <row>, <col>

Mouse Headfixing¶

Setup¶

Headfix the mouse using the 3D-printed parts:
MouseHeadFixTop.dxf
MouseHeadFixBottom.dxf
MouseHeadFixPost.dxf
Position under camera with:
Cortex visible
Bregma identifiable
Target region in field of view

ROI Placement¶

During preview, drag ROIs to:
Target brain region
Reference region (for dual ROI)
Positions are saved to config.ini after preview

Audio Setup¶

Speaker Requirements¶

Frequency response: 1-24 kHz
Small form factor for setup near mouse

Audiostream Configuration¶

from audiostream import get_output
from audiostream.sources.wave import SineSource

austream = get_output(channels=1, rate=44100, buffersize=128)
sinsource = SineSource(austream, 1000)
sinsource.start()

Power Considerations¶

Raspberry Pi¶

Recommended: 5V 3A power supply
Can power LEDs directly (with resistors)
Water valve may need external power

Jetson Orin¶

Use official power supply
Ensure adequate cooling
Monitor power consumption for GPU work

Safety Notes¶

Warning

Always use appropriate resistors for LEDs
Verify polarity before connecting
Keep water valve wiring separate from logic
Ensure proper grounding