Cell models & electrophysiology / Specimen 571654895
Cellular Electrophysiology Laboratory
Current clamp, membrane biophysics and passive cable spread in one laboratory.
Experiment 01
Current Clamp
Current steps through the pinned soma mechanisms of specimen 571654895: voltage traces, steady-state IV and f-I.
Somatic voltage
Shaded band: current step · spike event: upward -25 mV crossing, 2 ms refractory
Run
| Resting potential | mV |
|---|---|
| Step-end mean (last 50 ms) | mV |
| Spikes during step | |
| Rate during step | Hz |
| First-spike latency | |
| Input resistance (IV slope) | GΩ |
C dV/dt = Iinj − gleak(V − Eleak) − Σ gion(V − Eion)
Spikes: upward −25 mV crossing, linear interpolationSteady-state IV
Mean of last 50 ms of a 600 ms step · depolarizing points that spike omitted
f-I curve
Spike count in a 600 ms window · rate falls above ~160 pA: depolarization block · sweep computing
Soma parameters · specimen 571654895 · 34 °C
| Parameter | Value | Unit |
|---|---|---|
| gbar_NaV | 0.135437665631 | S/cm² |
| gbar_Ih | 2.45309363012e-05 | S/cm² |
| gbar_Im | S/cm² | |
| gbar_K_Pst | 0.0246324806865 | S/cm² |
| gbar_K_Tst | 0.0131737791041 | S/cm² |
| gbar_Kv3_1 | 0.0112786383416 | S/cm² |
| gbar_Ca_HVA | 0.000190393703451 | S/cm² |
| gbar_Ca_LVA | 0.000330344255932 | S/cm² |
| gbar_SK | 0.000386531602321 | S/cm² |
| cm | 3.662555837 | µF/cm² |
| g_pas | 5.26101819431e-05 | S/cm² |
| e_pas | -93.3142719865 | mV |
| gamma_CaDynamics | 0.00563040571915 | |
| decay_CaDynamics | 438.850778307 | ms |
| Membrane area | 843.356 | µm² |
Scope & provenance
| Geometry | One isopotential compartment · soma membrane area summed from the pinned morphology, 10 µm variant · no dendritic or axonal load |
|---|---|
| Not the full cell | Input resistance and excitability differ from the reconstructed neuron · quantitative agreement with the published model is not claimed |
| Integration | Same fixed-step solver and channel code as Cortex Laboratory · dt 0.025 ms · NEURON state convention |
| Calcium | CaDynamics active with fitted gamma and decay · SK reads updated intracellular calcium |
| Sweeps | Fixed protocol · 200 ms baseline · 600 ms step · computed in the browser · spiking points excluded from the IV line |
| Depolarization block | f-I rate falls above ~160 pA as NaV inactivates · a property of this single compartment, not a tissue prediction |
| Model status | Published fitted model mechanisms · no independent biological validation here |
| Source | Allen Institute model repository · Fitted parameters · Allen license |
| Equations & verification | Methods · Numerical verification |
Experiment 02
Membrane Biophysics
Steady-state gates, kinetics and ideal voltage-step responses of the nine pinned channel mechanisms at 34 °C.
Steady-state gates
mh
Time constants
mh
Ideal voltage-step gate response
mh
At clamp voltage · -40 mV
| Gate | x∞ | τ (ms) |
|---|---|---|
| m | 0.081911 | 10.027 |
| h | 0.10140 | 348.31 |
| Open fraction | 0.00068029 |
dx/dt = (x∞(V) − x) / τ(V)
x(t) = x∞ + (xhold − x∞) exp(−t/τ)Fitted conductance density · S/cm²
| Mechanism | soma | axon | apic | dend |
|---|---|---|---|---|
| NaV | 0.135437665631 | 0.391423228686 | 0.018153385589 | 0.000269503250592 |
| Ih | 2.45309363012e-05 | 4.47718493978e-06 | 6.29381730308e-06 | |
| Im | 0.000477587645461 | 0.00352002258658 | ||
| K_Pst | 0.0246324806865 | 0.097558288985 | ||
| K_Tst | 0.0131737791041 | 0.95791276734 | ||
| Kv3_1 | 0.0112786383416 | 1.09153333418 | 0.0743371325412 | 0.0161231658822 |
| Ca_HVA | 0.000190393703451 | 0.000165986709924 | ||
| Ca_LVA | 0.000330344255932 | 2.47216470503e-06 | ||
| SK | 0.000386531602321 | 0.0139246742459 |
Scope & provenance
| Kinetics | Same 34 °C functions as Cortex Laboratory · mixed-species mechanism sources |
|---|---|
| NaV | 12-state stationary distribution · open state O · no single τ · stationary solve, not upstream seqinitial |
| Voltage step | Ideal prescribed voltage · independent gates · fixed intracellular calcium · no membrane integration |
| Model status | Published fitted model · no independent biological validation here |
| Source | Allen Institute model repository · Fitted parameters · Allen license |
| Equations & verification | Methods · Numerical verification |
Experiment 03
Cable Explorer
Passive spread of voltage along a uniform sealed cable: length constant, steady state and step transients.
Steady-state voltage along the cable
Line: finite-volume solve · dots: analytic sealed-cable solution · max difference % of V(0)
Step transient
Cable properties
| Length constant λ | µm |
|---|---|
| Electrotonic length L/λ | |
| Membrane time constant τ | ms |
| First equalization constant τ₁ | ms |
| Input resistance, analytic | MΩ |
| Input resistance, numeric | MΩ |
λ = √(d·Rm / 4·Ri) τ = Rm·Cm
V(x) = I·R∞·cosh((L−x)/λ) / sinh(L/λ)
R∞ = √(rm·ri) Rin = R∞·coth(L/λ) τ₁ = τ / (1 + (π·λ/L)²)Configuration
| Geometry | Uniform cylinder · sealed ends · 128 compartments · lateral membrane only |
|---|---|
| Injection | Somatic end (x = 0) · held to 6τ |
| Solver | Finite-volume backward Euler · Hines tree · dt 0.025 ms · same integrator as Cortex Laboratory |
| Membrane | Pure leak · no active channels · rest -65 mV |
Scope & provenance
| Model | Uniform passive cylinder · sealed ends · lateral membrane only · no branches, spines, taper or active channels |
|---|---|
| Theory | Analytic steady state for a finite sealed cable with point current at one end, after Rall · transients are numeric only |
| Integration | Same finite-volume backward-Euler solver as Cortex Laboratory · dt 0.025 ms · 128 compartments · injection held to 6τ |
| Comparison | Numeric steady state shown against the analytic profile live · default parameters agree within 0.5% of V(0) |
| Defaults | Cortex Laboratory passive membrane: Rm 20000 Ω·cm² · Ri 150 Ω·cm · Cm 1 µF/cm² · rest −65 mV |
| Interpretation | A teaching model of passive spread, not a reconstructed neuron · dendrites in the cell atlas carry active mechanisms and branches |
| Equations & verification | Methods · Numerical verification |