The most significant technical challenge is synchronizing the clock of your computer with the luminance samples made by the USB device.
To allow your computer to determine exactly when samples were
acquired, a simple protocol involving timestamp exchange is
implemented between the host computer and the USB device. The host
sends a request to the arduino, keeping note of the time the request
was made (T_host_request). The lagtestino firmware responds to this
request by sending the current value of its clock (C_arduino). The
host records the time of arrival of this new data
(T_host_receive). By assuming that delays are symmetric and only
accepting responses that occur within a short latency (thus bounding
maximal error), the host calculates that the device's timetamp
occurred at T_arduino_estimate:
request_response_roundtrip_duration = T_host_receive - T_host_request
if request_response_roundtrip_duration < maximal_acceptable_error:
T_arduino_estimate = (T_host_request + T_host_receive) / 2
So T_arduino_estimate is the best guess as to when C_arduino was
sampled, in the host computer's timebase. After many such samples, we
have two corresponding vectors:
T = [ T_arduino_estimate[0], T_arduino_estimate[1], ... ]
C = [ C_arduino[0], C_arduino[1], ... ]
We can now model the relation between the two clocks with:
T = gain*C + offset
The values of gain and offset can be found by a least-squares fit
from the acquired vectors T and C. Doing so allows conversion from
any arduino clock value (C_arduino) to be directly converted to a
timestamp of the host computer.
This is concept is a simplification of the ideas contained in the IEEE 1588 specification but is sufficient for acheiving sub-millisecond timing precision between an arduino and unpriviledged software.