Appendix - GitHub Repository
Photoplasm on GitHub
The Photoplasm repository is now public!
github.com/ericview-dev/photoplasm
This is the living source of record for the project — hardware documentation, calibration scripts, the Quick Start Guide, and all supporting assets. Everything built during HTGAA 2026 is here, versioned and open.
Snapshot Notice
This document overview is a snapshot of working files in active development — for the latest versions, branch history, and releases, visit the public repository.
What the Repo Contains
Documentation (/docs)
The Quick Start Guide is structured as ten chapters and three appendices, all in Markdown.
| File | Title | |
|---|---|---|
| Ch. 1 | photoplasm_ch01_ssh.md | SSH Setup & VS Code Remote Development |
| Ch. 2 | photoplasm_ch02_github.md | GitHub & Version Control |
| Ch. 3 | photoplasm_ch03_wavelength_sensor.md | AS7341 Wavelength Sensor |
| Ch. 4 | photoplasm_ch04_led_ring.md | LED Ring · 470nm PWM Control |
| Ch. 5 | photoplasm_ch05_oled_mask.md | OLED Digital Image Mask |
| Ch. 6 | photoplasm_ch06_heater_perfboard.md | Incubation Heater Perfboard |
| Ch. 7 | photoplasm_ch07_system_integration.md | System Integration |
| Ch. 8 | photoplasm_ch08_gui_flask.md | GUI / Flask Web Interface |
| Ch. 9 | photoplasm_ch09_spaceplacer.md | SpacePlacer |
| Ch. 10 | photoplasm_ch10_camera_module.md | Camera Module |
| App. A | appendix_A_calibration_protocol.md | Calibration Protocol |
| App. B | appendix_B_feature_specification.md | Feature Specification |
| App. C | appendix_C_pinout_NS-03_v8.md | Pinout NS-03 v8 |
Calibration Scripts (repo root)
Three Python scripts, all validated on hardware:
| Script | What it does |
|---|---|
photoplasm_densitometer.py | 16-step Bayer ordered dither sweep — measures AS7341 response vs. OLED pixel density. Confirmed OLED optical neutrality at 470nm. |
photoplasm_cal01.py | Cumulative pie-wedge step wedge — builds a 360° dose gradient across the plate for H&D curve construction. |
photoplasm_cal02.py | Three-state irradiance calibration — display off / blank / all-white. |
Hardware Stack
The device is a 3D-printed cylindrical assembly. From illumination source to sensor:
| Component | Status |
|---|---|
| 470nm LED ring · 9× LEDs · GPIO18 PWM0 | ✅ Operational |
| OLED photomask · SSD1309 128×64 · SPI | ✅ Operational |
| 84mm agar culture plane | — |
| AS7341 spectral sensor · I²C 0x39 | ✅ Operational |
| Incubation heater · PTC · GPIO13 PWM1 · DS18B20 37°C | ⚠️ Wired · not yet bench-tested |
What’s Next
The hardware is operational and calibration scripts are validated. Remaining work:
- Calibrate Kc (irradiance coefficient) — required before biological stepwedge experiments
- Bench-test heater PWM1 and DS18B20 temperature loop
- Implement Flask GUI (Ch. 8) and camera module (Ch. 10)
- Run the biological stepwedge — characterize the H&D dose-response curve across toe, linear, and shoulder regions
That curve is the goal: a quantitative map of how Photoplasm translates light dose into gene expression. Everything built so far is the instrument.
Built at Makerspace Charlotte BioArt Studio · HTGAA 2026 · Eric Schneider