Here's the schematic for my Bee Counter test board with the functional units labeled to make them easier to discuss. This test board has the same circuitry as the larger board, but with only 4 gates instead of 44 to save a TON of time and money debugging it. I should warn you that I haven't seen it work yet, so there's nearly a 100% chance that it won't work as drawn, but I'm pretty confident the design is solid even if my wiring or resistor values are off a bit, or if I somehow specified chips that won't work together.
Click here to download the full size of the above Circuit.
To summarize, the 555 timer circuit (in red) puts out short pulses that will be used to pulse the sensor LEDs. The pulses are sent to the LED pulser circuit (green). There they are routed to each set of 4 LEDs (only 2 sets in this test board). This pulses the LEDs 4 at a time (purple), but this means that any signal from the sensors is pulsed as well. The SR Latches (orange) save a recorded signal (latching any high voltage) so the microcontroller can read the sensors without synchronizing the reading with the LED pulsing. After reading the state of each latch, the microcontroller will reset each latch so they're ready to record another measurement. The demultiplexer simply allows the microcontroller to read and write to the 88+ sensor pins (read and reset for each sensor) with a minimum number of microcontroller pins (as few as 15 pins for 44 sensors)
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