cyan-at / optogenetic-feedback-loop

Optogenetic feedback loop for shaping the behavior of cortical organoids

optogenetic-feedback-loop

Optogenetic feedback loop for shaping the behavior of cortical organoids

Contents

Array

Drives Raspberry Pi Zero GPIO connected to Serial to Parallel Converter Chips

• Serial Shift Register Chip: 8 bit, 7HC595 from NXP Semiconductors
  • datasheet:
    • https://cdn-shop.adafruit.com/datasheets/sn74hc595.pdf
    • https://datasheet.octopart.com/74HC595N-Philips-datasheet-7085704.pdf
• High-performance GPIO Library bcm2835: https://www.airspayce.com/mikem/bcm2835/
• Raspberry pi pinout reference: https://pinout.xyz/pinout/wiringpi

Organoid Simulation

• Predict organoid output based on array input, refine model with real organoid data

Supervisor Algorithm

• Hebbian Learning Feedback Loop
• Mediating connections between different organoids
• Simplified Difference Target Propagation (SDTP)

Communication Protocol

• Messages sent via UNIX network sockets
  • Master sends boolean values as a list inside Message
  • Array receives message and toggles LEDs

Graphics Library

• Display events in graphical user interface

System Architecture