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Simulation Parameters

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syorkp edited this page Apr 28, 2023 · 4 revisions

A list of simulation parameters and how they have been determined, with references. Also link specifically to env_variable keys.

Unmentioned parameters are set practically/arbitrarily.

Simple Parameters

Fish body:

  • Length - 4.4mm (Singleman & Holtzman, 2014)
  • Head diameter - set to match intraretinal distance.
  • Intraretinal distance - 0.5mm (Bianco et al., 2011)
  • Mouth diameter - 0.8mm (Set practically, should be lower)

Visual system:

  • UV photoreceptor num - 55 (At 8 d.p.f, fish have around 2,400 cones per eye (Yoshimatsu et al., 2020), so a 1D strip would be given by N=2sqrt(2400/pi) = 55.) NOTE: Think the justification for this changed at some point?
  • UV receptive field size - 0.76 degrees (Yoshimatsu et al., 2020)
  • Strike zone size, PR spacing etc. - Not sure, was recent addition.
  • Red photoreceptor number - 63 (UV:Red ratio of 0.87 in larvae 3-4dpf (Allison et al., 2010).
  • Red receptive field size - 0.76 degrees (assume same size as UV).
  • Eye vergence - 76.4 degrees for permanently converged eyes. (Bianco et al., 2011).
  • Visual field - 163 degrees.

Paramecia:

  • Diameter - 0.1mm (Van Houten, 2019)
  • Max turning rate - 0.04 radians per step (set practically to produce linear wavy).
  • Max reorienting rate - Pi radians per step (set practically to allow full reorientation within a step).
  • Slow gait speed - 0.5mms-1 (Hamel et al., 2010)
  • Fast gait speed - 1.0mms-1 (Hamel et al., 2010)
  • Jumping/escape gait speed - 10mms-1 (Paramecium turns sideways and moves several body lengths at this rate (Bray et al., 1992; Hamel et al., 2010), and therefore should only happen for a step.)

Predator:

  • Diameter - 6.4mm (conflicting info but think was to match onset of loom stimulus used in lab)

  • Speed - ? (Set practically to incentivise use of C-start escapes)

  • Initial distance - 18.2mm (Set practically to incentivise use of C-start escapes)

  • Step duration - 200ms (to match the average duration of a bout, including burst and glide phases (Severi et al., 2014)

Complex Parameters

Visual range:

  • background brightness - 0.1 (set practically to allow for sufficient noise in photon counts).
  • Light gain - 125.7 (set practically to allow 1.5:1 SNR at 10mm, and close to inf:1 SNR at 3.7mm to which fish have shown to initiate hunting, Bolton et al. 2019). NOTE, will need recalibrating.
  • Dark gain - 60 - (set practically to how 1.5:1 SNR at 3.7mm).

Capture restrictions - all set so that capture success spatial plots match strike zone plots (Raphael data):

  • Fraction capture permitted - 0.2
  • Permitted incidence deviation - pi/5

Motor effect noise (PPO only):

  • Set practically so that capture success spatial plots match strike zone plots (Raphael data).

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