Delete and rebuild the local TC_SPI_CS_N and TC_MINUS_FILT segments, connect U3’s AGND/DGND directly to C7/C8, then reroute the displaced signals. This is the least invasive option, preserves the other completed routing, and gives the MAX31856 short local decoupling returns without moving components.
I’ll surgically remove the two blocking signal segments, close U3’s AGND/DGND returns to C7/C8, rebuild the displaced signals, then clean copper and run final DRC plus an independent review.
Worked for 6 mins 21 sec
flux
9 hrs ago
The two U3 ground returns are now connected, and TC_MINUS_FILT has been rebuilt cleanly. The final TC_SPI_CS_N route timed out after its stale branches were removed, so I’m using the permitted cleanup routing pass on that single remaining airwire.
Worked for 14 mins 55 sec
flux
8 hrs ago
The surgical reroute succeeded for TC_SPI_CS_N, TC_MINUS_FILT, and U3 AGND. One airwire remains because the rebuilt chip-select trace blocks C8’s DGND escape.
I recommend moving and rotating C8 below U3; this creates a short, clean decoupling return without disturbing the rest of the board.
Scope: Instrumentation only. It heats and optically measures one externally prepared, target-specific RT-LAMP reaction per run in a sealed 0.2 mL PCR tube.
Develop the engineering foundation for a future research platform that can evaluate target-specific RT-LAMP assays for respiratory viruses. Separate COVID-19, influenza A, influenza B, or other target results require separate validated reactions and controls, or a future validated multiplex chemistry with distinguishable signals. The one-tube, one-color Rev 1 architecture cannot distinguish several targets in one reaction.
Rev 1 will prove only the reusable instrument functions: safe preheated isothermal incubation, repeatable time-series color measurement, standalone operation, fault handling, and export of engineering data. It will not prove a pathogen assay or a complete saliva workflow.
Intended Use
Indoor benchtop research and education.
Operated by the builder using established research-use-only reagents and procedures.
The user inserts a sealed reaction tube, closes the optical lid, selects a run profile, starts the cycle, and observes temperature, time, and color measurements.
The device must be labeled Research Use Only — Not for Diagnostic Use.
What the Device Should Do
Accept one standard 0.2 mL PCR tube.
Heat the reaction zone to a configurable isothermal setpoint, initially centered on 65 °C.
Hold temperature with a design target of ±0.5 °C after settling.
Run configurable 30–60 minute cycles.
Preheat the empty block, prompt for safe insertion of a room-temperature sealed tube, and start assay timing only after the reaction liquid reaches the validated temperature band.
Illuminate the tube consistently and measure color change without opening it.
Display measured temperature, setpoint, elapsed/remaining time, normalized color metric, heater state, and faults.
Allow the user to label each sequential run as sample, no-template control, positive control, or sample/process control and associate it with a run-set ID.
Store calibration constants and the last run summary locally.
Export raw time-series measurements through the service USB interface in CSV format.
Shut down the heater on sensor failure, overtemperature, timeout, lid-open condition, or firmware watchdog fault.
Main Features
Single light-tight optical chamber within a transparent learning enclosure.
Aluminum tube heater block with embedded heater and temperature sensor.
Controlled LED illumination and digital color sensor.
Small OLED display and pushable rotary encoder.
Rear low-voltage DC input from a certified external adapter.
Visible, connectorized internal subsystems for learning and service.
Optional service USB/debug connector; not required for normal operation.
System Architecture
The external adapter powers an input-protection stage. A switched heater rail drives the resistive heater through a MOSFET. A regulated logic rail powers the microcontroller, display, color sensor, memory, and safety sensing. The microcontroller performs closed-loop temperature control, sequences optical readings, operates the UI, records calibration, and enforces independent fault limits.
Hardware Subsystems
Power Input and Protection
Certified external low-voltage DC adapter; preliminary architecture assumes 12 V nominal.
Reverse-polarity protection, input fuse or resettable protection, transient suppression, power switch, and bulk capacitance.
Thermal Control
Machined or drilled aluminum block shaped for a 0.2 mL PCR tube.
Low-voltage resistive cartridge or embedded heater, MOSFET switched with PWM.
Primary block temperature sensor plus an independent overtemperature cutoff path.
Thermal insulation between block and printed enclosure.
Optical Measurement
Opaque chamber around the tube despite the transparent outer enclosure.
Controlled broad-spectrum or RGB LED illumination.
Digital RGB/clear color sensor viewing the reaction volume through a repeatable geometry.
Dark and reference calibration routines; ambient light rejection by enclosure and measurement sequencing.
Compute and Storage
Low-cost microcontroller with ADC, timers/PWM, I2C, nonvolatile memory, watchdog, and service programming/debug support.
No wireless connectivity in Rev 1.
User Interface
Small I2C OLED.
Pushable rotary encoder for selection, adjustment, start, cancel, and acknowledgement.
Optional buzzer for completion and fault alerts.
Safety and Fault Handling
Heater defaults off at reset and during programming.
Hardware-biased MOSFET gate pulldown.
Independent thermal fuse or thermostat in series with heater power.
Firmware bounds for temperature plausibility, heating rate, maximum heater-on time, and maximum block temperature.
Lid interlock or lid-presence switch prevents optical measurement and can pause/abort heating.
Interfaces and Connections
Table
Interface
Purpose
12 V DC input
External certified adapter
Heater output
PWM-switched high-current load
Primary temperature input
Closed-loop block temperature
Independent thermal cutoff
Hardware heater interruption
I2C bus
OLED, color sensor, optional EEPROM
Encoder A/B/SW
User input
Lid switch
Optical and thermal safety state
SWD/UART/USB service port
Firmware programming and debug
Assay and Sample Interface Requirements
Rev 1 accepts a sealed nominal 25 µL reaction in a 0.2 mL PCR tube; a validated assay may define another volume within the tube and optical geometry limits.
Collection method, saliva pretreatment, extraction or inactivation chemistry, sample input volume, and acceptable pH/buffer conditions are assay-level inputs and must be documented before biological testing.
The instrument records the pre-incubation optical baseline. A baseline outside the assay-specific calibrated range is reported as an invalid input condition rather than amplification.
A run set is interpretable only when its required target-specific positive, negative, and sample/process controls pass their predefined criteria.
The instrument reports research measurements and control status, never a patient diagnosis.
Power and Runtime Expectations
Wall-powered; no battery or charging circuitry.
Preliminary maximum input power target: 30 W or less.
Normal run dominated by heater power during warm-up; lower duty cycle at steady temperature.
Electronics remain powered after a run while the heater is disabled.
Power Tree and Power Budget
12 V protected input.
Direct protected 12 V heater rail, switched by an N-channel MOSFET.
12 V to 5 V buck rail for peripherals if required.
5 V to 3.3 V regulation or a direct 12 V to 3.3 V buck for logic.
Detailed preliminary estimates are maintained in the Power Budget project file.
Manufacturing and Assembly Expectations
One-off learning prototype with room for measurement and rework.
Prefer readily available components and hand-accessible connectors.
PCB assembly may be outsourced; mechanical heater block and enclosure assembled manually.
Include labeled test points for input power, logic rails, heater gate, temperature sensor, I2C, reset, and ground.
Use a 2-layer board if noise and thermal routing permit; move to 4 layers only if layout review justifies it.
Firmware-Relevant Hardware Requirements
Deterministic PWM and periodic temperature sampling.
PID or bounded proportional control with configurable setpoint and duration.
Color sampling with LED-off dark measurement and LED-on measurement.
Calibration storage with versioning and reset-to-default function.
Watchdog, brownout handling, sensor plausibility checks, and fault logging.
Bootloader/programming access without opening the optical chamber.
Physical Design Expectations
Transparent 3D-printed educational enclosure with visible internals.
Opaque removable optical chamber and hinged light-tight tube lid.
Sloped front panel with OLED and rotary encoder.
Rear DC input and service access.
Screw-fastened removable base.
Preliminary outer envelope: approximately 140 × 100 × 75 mm; to be refined after part selection.
Preliminary PCB envelope: up to approximately 100 × 70 mm; to be refined after enclosure CAD.
Hot surfaces inaccessible during normal operation; tube remains removable after cooldown.
Important Design Decisions
Colorimetric rather than fluorescence detection for Rev 1.
One 0.2 mL PCR tube rather than multiple wells.
Standalone UI rather than computer-dependent operation.
External certified low-voltage adapter rather than internal mains, USB-PD, or battery power.
Transparent learning enclosure with a separate opaque optical chamber.
Measurements are presented as research data, not a clinical positive/negative diagnosis.
Assumptions
Initial assay profile uses approximately 65 °C for 30–60 minutes; actual validated assay instructions override this.
The colorimetric chemistry is compatible with optical sensing through the selected PCR tube.
Sample preparation and sealed-tube handling occur outside the instrument.
The initial biological workflow and saliva preparation method are intentionally unresolved; schematic capture must not embed a fixed color threshold or disease-specific claim.
Exact heater wattage, optical wavelengths, sensor choice, and adapter rating will be selected after thermal and optical characterization.
Acceptance Criteria for Rev 1
Warm from 20–25 °C ambient to 65 °C within 10 minutes with a representative sealed tube or thermal dummy.
Maintain measured block temperature within ±0.5 °C for at least 30 minutes after settling.
After insertion into a preheated block, a nominal 25 µL liquid thermal dummy reaches the validated 65 °C band within 120 seconds; assay timing begins at that point.
Liquid temperature remains within ±0.5 °C of the assay target during the timed interval after block-to-liquid offset calibration.
Across at least five representative PCR tubes, liquid-temperature variation at steady state is no more than 1.0 °C peak-to-peak.
Condensation or evaporation does not obscure the optical region or reduce the reaction-zone liquid volume by more than 5%; failure triggers a heated-lid design review.
Hardware cutoff prevents sustained block temperature above the selected safe limit.
Repeatable normalized color measurements from fixed reference samples with less than 2% short-term variation under closed-lid conditions.
OLED and encoder support setup, start, status, abort, completion, and fault workflows.
No exposed mains voltage and no normally accessible hazardous hot surface.
Instrument acceptance criteria above verify the reader only. Separate assay-validation criteria must cover limit of detection, inclusivity, cross-reactivity, positive/negative agreement, invalid rate, controls, specimen type, and sample preparation before any assay-performance claim.
Change Notes
Rev 1 scope approved as a standalone, single-tube, colorimetric reader with a transparent learning enclosure, OLED/encoder UI, and external low-voltage adapter.