B.O.L.T. — Budget Optogenetic Light Tool

Control 4 independently-addressable 12V LED strip channels from a laptop GUI, for optogenetic illumination of multi-well plates.

Files

• bolt_firmware/bolt_firmware.ino — Arduino Uno sketch. Upload this via the Arduino IDE.
• bolt_gui.py — Control GUI, runs on the laptop (Windows or Mac).
• BOLT_Housing_STLs/ — 3D-printable housing and plate accessories (see below).

Bill of materials

Wiring and power

Each of the 4 LED strip channels is a 12V LED strip, wired through an LED connector into an 8-pin screw terminal plug, then into the transistor board, which switches each channel under control of the Arduino (connected to the transistor board's own 8-pin screw terminal plug). Two separate power supplies are used:

• A 12V adapter powers the transistor board (and, through it, the LED strips).
• A 9V adapter powers the Arduino microcontroller.

This same wiring and LED base is compatible with both the 24-well and 96-well configurations — only the plate-specific housing parts (light isolator and lid, see below) change between the two.

The default pin mapping is:

Channel	Arduino Pin
1	D3
2	D9
3	D10
4	D11

Each channel's pin is reassignable from its Pin dropdown in the GUI (see "Using the GUI" below), to any PWM-capable pin: D3, D5, D6, D9, D10, or D11.

3D-printed housing (STLs)

BOLT_Housing_STLs/ contains the printable parts for the physical rig, each designed around a specific commercial plate:

• 24-well parts fit the Corning Costar 24-well plate (catalog #3524).
• 96-well parts fit the Greiner Bio-One 96-well flat-bottom clear plate (catalog #655101).

A different plate brand, or a different well shape/catalog number, may not fit without modifying the STLs.

File	Purpose	Designed for
electronics_housing.stl	Enclosure for the Arduino + transistor board	Both plate formats
LED_base.stl	Houses the 4 LED strips at the spacing the device requires	Both plate formats
plate_elevator.stl	Lifts the plate to allow illumination from the LEDs below, and secures the device to the incubator	Both plate formats
96-well_light_isolator.stl	Isolates the light output from each of the 4 LED strips, one per plate quadrant; the 96-well plate sits secured on top of it	96-well plate
96-well_lid.stl	Lid that sits over the plate to prevent light scattering over the wells	96-well plate
24-well_light_isolator.stl	Isolates the light output from each of the 4 LED strips, one per plate quadrant; the 24-well plate sits secured on top of it	24-well plate
24-well_lid.stl	Lid that sits over the plate to prevent light scattering over the wells	24-well plate

The parts stack in this order, bottom to top: electronics_housing.stl (holds the Arduino + transistor board) → LED_base.stl (the 4 LED strips) → plate_elevator.stl → the light isolator (96- or 24-well, with the plate secured on top of it) → the matching lid.

Print all parts at a 0.2mm layer height, in an opaque filament (e.g. black PLA/PETG) — the light isolators and lids exist specifically to block stray/ambient light and prevent cross-talk between wells, so translucent or light-colored filament defeats their purpose. Supports are only needed for plate_elevator.stl; the other parts print fine without them in a standard FDM orientation. Check wall thickness against your printer's nozzle size before scaling, and verify fit against the specific plates above before printing a full batch.

One-time setup

Arduino

1. Open bolt_firmware/bolt_firmware.ino in the Arduino IDE.
2. Select Board: Arduino Uno, the correct Port.
3. Click Upload.
4. Once uploaded, the Arduino can run from the 9V adapter (see "Wiring and power" above) — the laptop only needs to be connected via USB when you want to configure or start a run.

Laptop (Windows or Mac — same steps)

1. Install Python 3 if you don't have it (python.org).

2. Open a terminal in this folder and install the GUI as a command:

   pip install .
   

   (On Mac you may need pip3 install ..)

3. Run it from any terminal, any time, on either OS:

   bolt-gui
   

   Alternatively, without installing, you can always run it directly:

   pip install pyserial
   python bolt_gui.py
   

Using the GUI

1. Connect: pick your Arduino's serial port from the dropdown and click Connect. (On Windows it'll look like COM3; on Mac, something like /dev/cu.usbmodem....)
2. Configure each channel: tick Enabled, set Intensity (1–255) for the peak brightness of each individual flash, and set the Duty cycle (%) spinbox for how often it flashes — or set On/Off directly instead (switch the units dropdown next to them between ms and s). All three stay in sync (see "How intensity works" below); use whichever is more convenient. Tick Continuous to skip pulsing entirely and run at full brightness (100% duty) — your Duty cycle/On/ Off settings are locked but kept underneath, and come back when you untick it. The Pin dropdown picks which Arduino pin that channel uses (see "Wiring and power" above for the default mapping).
3. Duration: leave "Same duration for all channels" checked and set one value, or untick it to give each channel its own duration. 0 means "run until you press STOP."
4. Delayed start (optional): tick this and set a delay in seconds — after you press Start, the Arduino will count down, then begin illumination on all enabled channels at exactly the same moment.
5. Send Protocol to Arduino: pushes your current settings to the board.
6. Start: begins the experiment (after the delay, if set). All enabled channels start their first ON phase together.
7. STOP: immediately turns everything off, any time.
8. Save Protocol... / Load Protocol...: stores your full configuration (all 4 channels + duration + delay settings) as a .json file you can reuse for repeat experiments.

How intensity works

Two independent controls set how bright a channel looks, and they answer different questions:

• Intensity (1–255) — how bright each individual flash is at its peak (PWM level, analogWrite). This is a straightforward hardware dimmer.
• On/Off timing — how much of the time it's flashing at all. There's no separate "mode" to pick — every channel is either pulsing or continuous, decided automatically from the timing you set. Three linked controls all describe the same underlying on/off pattern, and editing any one updates the others to match:
  • Duty cycle (%) — a spinbox (0.5–100%, in 1% steps, arrows or typed) for the percentage of time spent flashing. Changing it recomputes Off at the current On.
  • On / Off — the flash width and dark gap themselves, typed directly and shown in whichever unit (ms or s) the small dropdown next to them is set to. Changing either recomputes the duty cycle percentage to match.
  • Continuous — a checkbox that skips pulsing entirely and forces full-time illumination (100% duty), without discarding your Duty cycle/On/Off settings — it just locks them and shows what they'd be doing again once you untick it.
  • Whenever a channel is continuous, the On box shows ∞ instead of a number — there's no fixed on-width to show once a channel never turns off. The Off box shows N/A too, since the dark gap is being skipped entirely.

The two axes multiply together: 50% duty cycle at Intensity 128 looks, on average, about a quarter as bright as continuous at Intensity 255.

The GUI shows the current duty cycle (or "continuous") next to each channel's on/off controls. In the LED Strip Preview panel, each strip is labeled with its PWM level (Intensity, 1–255) and duty cycle (%) side by side, and shaded by PWM level alone — a brighter strip means a brighter flash, regardless of how often it flashes. The timeline graph below draws several real pulse cycles to scale, colored the same way by each flash's own peak brightness — a solid bar for continuous channels, or the actual on-pulses against their dark gaps for pulsing ones (Simulate animates the strips above it in real time, at the speed you set) — a quick way to catch a misconfigured channel before committing hardware time to a multi-hour run.

Notes

• Timing runs entirely on the Arduino itself once started, so it won't drift or stop if the USB cable is unplugged or the laptop sleeps — useful for long unattended runs. You only need the laptop connected to configure and press Start/Stop.
• Intensity (1–255) is plain PWM, not calibrated to irradiance; if you want mW/cm² values, measure output at a few Intensity settings with a power meter and add a calibration curve to the GUI.
• All four channels run independently — just configure each panel's intensity, on/off timing, pin, and (optionally) per-channel duration separately.