Microcontroller Timing and Data Acquisition

The instrument timing and measurement of the photodetector amplifier output are handled using an LPC-Link2 board, which is based on the LPC4370 microcontroller IC.

This inexpensive ($20) board has the primary advantages of having an exceptional on-chip 12-bit ADC with sampling speeds up to 80 Msps and dual-core Cortex M4/M0 architecture, as well as other innovative peripherals such as GPIOs with optionally enabled anti-glitch filters and programmable slew rate. As explained in Section 2.1.1, the TGF measurement principle relies on precise timing of excitation and detection pulses. The MCU board controls the system timing by generating these pulses at its peripheral GPIO pins to pulse

the laser and turn on the photodetector, respectively, as well as by initiating its internal ADC sampling after the photodetector has turned on.

Figure 2.5(a) shows the overall relationship of the main timing and control signals involved in the system. The internal timers of the MCU control the pulses that appear on GPIO1 and GPIO2. As described in Section 2.2.2, GPIO1 serves as the input to the laser driver circuit, thus creating the main excitation light pulse for the system. GPIO2 is used to turn on the time-gated photomultiplier tube (PMT) when its voltage goes high, and therefore serves as the main detection pulse for the system. After a short delay to allow the PMT to turn on completely, the MCU triggers its ADC to begin sampling until the detection pulse ends, at which time the ADC sampling ends and the PMT is turned off by a low signal on GPIO2. The signal input to channel 0 of the high-speed ADC (ADCHS0) is the amplified output of the PMT detector.

The timing diagram in Figure 2.5(b) shows the temporal relationships between these signals, as well as the MCU timer parameters that can be used to quickly adjust the delays between events. The MCU timer directly controls the lengths of T, t1, t2, t3, and tsamp. Timing parameter T corresponds to the repetition period of the sequence of timing events, or the reciprocal of the repetition frequency (T = 1/frep), which is limited by the PMT gate circuitry to less than 10 kHz, according to the Hamamatsu 11706-20 datasheet. The excitation pulse begins at the start of the timing sequence, so parameter t1 defines the length of time after which the excitation pulse ends, and therefore the ratio t1/T corresponds to the duty cycle of the laser pulse. Parameter t2 corresponds to the time at which the PMT gate is turned on, so the delay between the laser turn-off time and the PMT turn-on time is defined as (t2 – t1). Timing parameter t3 is the time at which the MCU triggers its internal

Figure 2.5. (a) Relationship between important electronic signals and hardware connections. (b) Timing diagram showing the temporal relationships among electronic signals.

ADC to begin sampling, which allows for a short delay of (t3 – t2) to allow the PMT to turn on and to allow settling of the PMT gate circuit switching noise. The value (t3 – t1) therefore corresponds to the total delay between the end of the excitation pulse window and the start of the detection pulse window. The length of the detection window is not directly controlled by the timer but is instead ended after a period of time, tsamp, when the desired number of samples has been obtained by the ADC. At this time, the ADC stops sampling and the PMT is automatically turned off, and nothing happens until the start of the next period of the timing sequence. Table 1 summarizes these and other important parameters of the system.

A high-level logic flow diagram of the program execution is shown in Figure 2.6.

The program begins with the initial setup of the MCU peripherals, including the timers, ADC, I²C interface, etc. and the laser is initially turned off and disabled. An I²C OLED screen then prompts the user to begin the program by pressing the start button on the driver board, and the program awaits the user input. When the start button is pressed, the data buffers are cleared, and the ADC and timers are started. The main program then enables timer-based interrupts and then enters a loop that checks if ADC samples are available, in which case the available data will be processed. The timer-based interrupt shown to the right of the logic flow diagram executes the processes indicated in the timing diagram by turning the laser off, turning on the PMT gate, triggering ADC sampling, turning off the PMT gate, and turning the laser on at the appropriate times. Because the laser is initially disabled, the first dataset does not involve laser pulsing, but is instead collected in order to obtain the average background signal, which is later removed from the data obtained with the laser enabled. The first loop continues until the full dataset is obtained, at which time the laser is enabled, and the process repeats to obtain the second dataset which represents

Figure 2.6. Overall logic flow diagram of the microcontroller program. The main loop is shown to the left, while the right side shows the execution of the interrupt service routines.

the fluorescence signal from the sample. Once both sets are obtained, the program disables the interrupts, timers, and ADC, then completes the data processing and displays the output on the OLED screen. It then returns to waiting for the start button to be pressed again.

Thus, two datasets are obtained which correspond to the absence or presence of probe excitation, which can then be compared to determine the fluorescence intensity. Appendix 3 contains additional information on the MCU program.

2.3 Copper (II) Fluorescence Quenching Assay