Table 1. Parameters of the SPR model used to generate synthetic datasets.

Here we show both range of values we tested and baseline value that was used when we varied another parameter. Note that our simulations are non-dimensionalised, using the width of a single rod as the characteristic lengthscale and the time taken for an isolated rod with self-propulsion force ν = 1 to move a single rod width as the characteristic timescale.

Parameter symbol	Parameter name	Value(s)
A	Area of simulation domain	10,000
f 0	Stokesian friction coefficient	1
N	Number of rods	700 (baseline) [300, 500, 700, 900, 1100] (variable)
ν	Self-propulsion force	1 (baseline) [0.7, 0.85, 1, 1.15, 1.3] (variable)
ΔT	Time between sampled timepoints	10 (baseline) [5, 7.5, 10, 12.5, 15] (variable)
σ r	Standard deviation of positional measurement noise	0.02 (baseline) [0.02, 0.1, 0.2, 0.4, 0.6] (variable)
σ ϕ	Standard deviation of orientational measurement noise	0.02 radians
σ a	Standard deviation of length measurement noise	0.1 (baseline) [0.05, 0.1, 0.2, 0.4, 0.6] (variable)
σ I	Standard deviation of fluorescence measurement noise	1 A.U. (baseline) [0.5, 1, 2, 4, 6] A.U. (variable)