Stimulus recipes¶

This page is a practical cookbook of stimulus patterns you can run with Spikeling. Each recipe states:

what to select in the GUI
what to set
what it teaches
what to look for in Vm and spikes

Spikeling supports two main stimulus pathways:

Current stimulus: inject the waveform directly as input drive (current clamp logic)
Light stimulus: drive an LED (stimulus output → LED cable) and stimulate the photodiode pathway

For background on stimulus modes, see: Concepts → Stimulus protocols.

Before you start (recommended setup)¶

Pick one neuron mode and keep it fixed during a recipe.
Start with:
injected current = 0 (centre detent / patch clamp neutral)
noise = off (unless the recipe is about noise)
synapses = off (unless the recipe is about synapses)
Display:
Vm
Stimulus (or the current trace if you route stimulus as current)
Optional: Total input current (Itot)

Teaching rhythm

For each recipe: make students predict the response, then run it, then explain what changed.

Recipe 1 — Single step (classic current clamp protocol)¶

Use: threshold finding, adaptation, F–I curves
GUI mode: Steps
Route: Current

Settings (suggested)¶

Baseline: 1 s
Step duration: 2–5 s
Return to baseline: 1 s
Step amplitude: start small and increase

What to look for¶

Vm depolarisation/hyperpolarisation during the step
spikes appear once the step crosses threshold
adaptation: spike rate often slows over time during a long step

Recipe 2 — Step family (build an F–I curve)¶

Use: excitability quantification
GUI mode: Steps
Route: Current

Settings¶

Run a sequence of step amplitudes (e.g., 6–10 levels), keeping duration fixed.

Measure¶

spike count or firing rate during each step
plot firing rate vs step amplitude

Recipe 3 — Pulse train (frequency vs strength)¶

Use: recruitment, frequency following, reliability
GUI mode: pulse/square train (or square-like train via your GUI controls)
Route: Current (or Light for flicker teaching)

Settings¶

Set pulse strength moderate
Sweep frequency (e.g., low → high)
Then fix frequency and sweep strength

What to look for¶

some frequencies produce reliable time-locked spiking
at high frequencies, Vm may integrate or spikes may fail depending on mode

Recipe 4 — Sine wave (subthreshold resonance)¶

Use: membrane filtering, resonance intuition
GUI mode: Sine
Route: Current

Settings¶

Use small amplitude to keep Vm subthreshold
Sweep frequency manually or run several fixed frequencies

What to look for¶

Vm oscillation amplitude depends on frequency and neuron mode
some modes show stronger response in certain frequency bands

Note

This is best as a demonstration unless students already know resonance/impedance concepts.

Recipe 5 — Triangle wave (rate-of-change and threshold crossing)¶

Use: compare rising vs falling phases; “when does threshold get crossed?”
GUI mode: Triangle
Route: Current

Settings¶

Moderate amplitude
Low–moderate frequency

What to look for¶

spikes often cluster near the peaks (depending on mode)
threshold crossing can differ on rising vs falling ramps

Recipe 6 — Chirp / ZAP sweep (frequency probing)¶

Use: resonance, frequency preference, dynamic response
GUI mode: Chirp (linear or exponential; amplitude increase variants if available)
Route: Current

Settings¶

Keep amplitude subthreshold at first
Sweep over a wide band (e.g., low → high)

What to look for¶

Vm response changes across the sweep
some modes show “preferred” frequency ranges with larger Vm deflections

Recipe 7 — Noise stimulus (variability under controlled conditions)¶

Use: stochastic spiking, jitter, threshold probability
GUI mode: Noise
Route: Current

Settings¶

Set a small depolarising bias current so Vm is near threshold
Increase noise amplitude gradually

What to look for¶

intermittent spikes appear without changing mean input
spike timing becomes variable
rate increases with noise amplitude

Recipe 8 — On-board square stimulus (fast classroom demo)¶

Use: immediate hands-on demonstration
Source: on-board square stimulus generator
Controls: frequency + strength knobs (board)

Workflow¶

Keep current injection at zero initially.
Increase stimulus strength until Vm deflections are clear.
Increase frequency and observe changes in spiking reliability.

What to look for¶

easy “knob-to-trace” intuition
quick illustration of strength vs frequency effects

Recipe 9 — Light flicker (sensory-style stimulation)¶

Use: visual sensory analogue; polarity inversion with Photo-gain
Route: Light

Two common setups¶

Controlled LED: stimulus output → LED cable → photodiode
External LED source: any modulated light aimed at the photodiode

Settings¶

Start with modest Photo-gain
Use square pulses or a pulse train to deliver flicker
Flip Photo-gain sign to show excitatory vs inhibitory sensory drive

What to look for¶

same light can depolarise or hyperpolarise depending on gain sign
photoreceptor dynamics (decay/recovery) shape response to flicker

Recipe 10 — Synaptic drive bursts (postsynaptic recruitment)¶

Use: integration, coincidence, E/I balance
Source: presynaptic unit spikes (or emulator auxiliary neuron)

Workflow¶

Create presynaptic spiking bursts (increase presynaptic drive briefly).
Set postsynaptic neuron below threshold.
Increase synapse gain until bursts recruit postsynaptic spikes.

What to look for¶

burst summation is more effective than isolated spikes
inhibition can veto recruitment

Recipe 11 — “Design your own stimulus” (student capstone)¶

Use: experimental design thinking
Goal: students build a stimulus to test a hypothesis.

Example hypotheses: - “This mode adapts strongly, so a long step will slow firing.” - “Noise increases spike-time jitter but does not strongly change mean Vm.” - “This neuron responds differently to slow vs fast oscillatory inputs.”

Student checklist: - write the hypothesis - choose waveform type - choose amplitude and timing - record one dataset - compute one metric - interpret results

Practical tips¶

If you are confused, disable everything except one input pathwa