Open the Neural Interface Laboratory → — twelve active human cells, one finite-contact shank, full membrane replay, recordings and spike rasters.

Scientific evidence for this experiment

Field: Analytical point-source conductor; finite contact and shank boundaries are absent.
Native: Selected point-source reference cases exist. This panel does not certify the current configuration.
Refinement: Historical firing-boundary convergence failures remain unresolved; no general threshold accuracy claim.
Propagation: Not established by local crossings or somatic waveform evidence.
Selectivity: Not established. Synthetic axon and tissue assumptions limit interpretation.
Biological: Not validated against independent experiments.

Finite-contact validation results and limitations

Cortex Laboratory · single human cell

From membrane to contact.

Place an array, thread or shank. Follow calculated currents through a shared cortical scene.

Equations, evidence & scope →

Human cortical cells · published active modelsReconstructed dendrites · synthetic axon stub · no independent experimental validation

Published cells · no repeated specimens

Choose a neuron

Browse the Cell Model Atlas →

16 distinct human specimens. Each keeps its own reconstructed dendrites, published fitted membrane parameters and source-prescribed axon stub. Cortical region, layer and cell class remain source identities regardless of placement.

Cell typeDatasetSource layer Also in Finger AtlasTarget specimen

Selected: Human temporal L2 spiny cell · 571654895. Pyramidal / spiny excitatory · Human neocortex, L2; surgical tissue · Allen human EAP · Mosher 2020. Published source

Measured human dendrites and published fitted channels; source-prescribed synthetic 60 µm axon stub. Numerical comparisons do not establish biological or spatial-selectivity validation.

Finger Atlas specimens and morphology-only references

The atlas’s Allen specimen 508378649 is included here with its own matching published active fit. Nine other measured Allen reconstructions and twelve H01 neurite references remain available for anatomical inspection in the atlas; they have no matched electrical model in this library. Their firing response is unknown here. The atlas’s procedural DRG, spinal, thalamic and receptor illustrations are not counted as measured specimens.

Inspect Finger Atlas anatomy · Atlas provenance · Measured H01 reference pack

First run · a one-minute guide

Start with one reconstructed human cell and its original intracellular soma-spike example. Run the experiment, then replay voltage across its soma, dendrites and axon stub. Choose a patch-clamp current step for repeated firing, or an array example for electrode stimulation.

Choose an example, read its reset notice and click Load example.
Inspect the pial depth and contact distances. The source and return move with the array.
Click Run experiment. The active cell first undergoes 100 ms of numerical conditioning.
Replay slowly and use Next soma event for threshold crossings. Array examples also offer Phase 1 and Phase 2. Compare membrane mV, contact µV and source µA.
Pin a baseline, load its comparison example, rerun, and inspect changed settings and signal differences.

Geometry or input edits require a new run. View controls and signal-component selection do not. All examples describe this single-neuron model.

1 / Choose example

Curated example

Follow a soma spike and its separately calculated extracellular recording.

The same 5 ms input is increased to +1.2 nA; all other settings match the subthreshold intracellular example.

Loading replaces the neuron model, anatomy, implant and neuron positions/orientations, tissue, membrane, contacts/reference, input and numerical settings with the complete example. The current result is cleared; run again. A pinned baseline is retained.

Current settings match this example.

Expected behavior & verification

One upward soma crossing of −25 mV is detected in this 40 ms experiment. Earlier crossings can occur in the synthetic axon stub. These event criteria do not identify a measured biological initiation site.

Numerically reproduced with the laboratory solver; exact configurations and measured results are in the examples benchmark. Spiking waveforms and extracellular thresholds are not certified spatially converged; see the refinement report. This is a model-specific calculation, not independent biological validation or a real-device stimulation recommendation.

Neuron model · Human temporal L2 spiny cell · 571654895

Measured human dendrites and published fitted channels; source-prescribed synthetic 60 µm axon stub. Numerical comparisons do not establish biological or spatial-selectivity validation. Model source →

34 °C · fitted channel distributions · 100 ms initialization conditioning. Detailed runs can take several seconds; repeat runs reuse identical conditioning.

ProtocolSoma current · nA

Includes a point bath return at [2000, 2000, -500] µm. This is distinct from extracellular stimulation.

Onset · msCurrent step duration · msRecording length · ms

A sustained current step can produce repeated spikes and adaptation. Choose “200 ms current step” or “500 ms current step” above, then Load example and Run. Set recording length beyond onset + step duration to include recovery. This is ideal somatic current clamp; pipette resistance and clamp electronics are not modeled.

2 / Place implant & recording

Implant geometry

100 physical shanks · 96 nominal channels. Ideal point sensing at apices; exposed areas and channel map unknown.

Changing implant resets its pose and recording pair, keeping the neuron and solver settings. For recording-only implants, extracellular polarization switches to intracellular current clamp. Loading a curated example restores its Utah array.

X translation · µmY translation · µmSubstrate origin Z · µm

Tilt X · °Tilt Y · °Rotate Z · °

Pia is Z = 0; +Z points into cortex. X/Y are lateral. Rotation applies X, Y, then Z about the tissue-facing substrate center, before translation. Layers are anatomical guides.

Mean tip depth below pia · µm

Apex depth range: 1500.00–1500.00 µm. Without tilt, tip depth = substrate Z + 1500 µm.

Recording site ARecording site B

Catalog geometry & sources →

Neuron placement & advanced physiology

Human temporal L2 spiny cell · 571654895 in an illustrative slab; the published model uses a synthetic active axon stub. Placement depth does not change its cortical identity.

Cortical thickness · µmSoma X · µmSoma Y · µmSoma depth · µmCell rotation X · °Cell rotation Y · °Cell rotation Z · °Conductivity · S/m

Capacitance, axial resistivity and channel densities use the pinned source model and vary by section type. Read model conventions →

Advanced numerical settings & files

Timestep · msMaximum segment length · µmOutput sample interval · ms

Output sampling changes saved plots, replay and exports, not integration or internal spike detection. Longer runs remain limited to 64 MiB of numeric output. At the default 40 µm mesh, use 0.1 ms for a 250 ms recording, 0.25 ms for 600 ms, or 0.5 ms for 1200 ms. Coarser output can miss spike peaks; use a shorter recording with finer output for waveform inspection. No resolution is changed automatically.

Neurite source model

Ready to calculate.

Pia Z = 0 · +Z into cortex
Physical anatomy · enlarged contact guides

100 µm

Electrical overlays Cutaway layers OrthographicAnatomy opacity

Loading 3D workspace…. Thin lines mark neurite centers; crosshairs mark recording sites. Colors show membrane voltage from −100 to +40 mV. The selection marker identifies the inspected compartment.

Contact tips Applied tissue potential Membrane coloring Contact labels

Display controls update immediately; they do not alter the experiment. Enlarged spheres (stimulating) and diamonds (recording) are visual guides, not contact dimensions.

Neuronal membrane voltage Vₘ

-100 mVVₘ+40 mV

Absolute voltage across membrane; −100 to +40 mV. 0 compartments saturated at this sample.

Ideal recording-contact potential · neural

-1.00e-9 µV0+1.00e-9 µV

Auto peak across both contacts and all run samples. 0 contacts saturated now. Each marker is A or B relative to infinity, even when the plot shows A − B.

Neural = potential generated by total membrane currents through the point/line forward model. Applied = stimulation sources or current-clamp bath return. Total = neural + applied. Tissue slices show only applied array stimulation; no neural volume field is inferred from recording traces.

Slice geometry & color scales

Slice orientationSlice extent · µmCenter offset from soma X · µmCenter offset from soma Y · µmCenter offset from soma Z · µmSlice opacity · 0.24Tissue scaleTissue ±limit · mVRecording scaleRecording ±limit · µV

Slice center [-100, -200, 1500] µm. Each slice samples 25 × 25 points with linear color interpolation. Cells intersecting a 25 µm source exclusion sphere are omitted; holes can exceed the sphere by one grid cell. No distance clamp or finite-contact regularization is used.

Run the experiment to inspect electrical values.

One unbounded homogeneous conductor; ideal point contacts. No electrode impedance, finite surface voltage, shank obstruction, layered conductivity or acquisition electronics.

I0.0000–0.2400 mmII0.2400–0.6400 mmIII0.6400–1.84 mmIV1.84–2.00 mmV2.00–3.00 mmVI3.00–4.00 mm

Layer fractions are illustrative. CSF and white matter are anatomical guides; all electrical calculations use one homogeneous conductor.

Inspect coordinates & membrane

Compartment

Center / µm-100.00, -200.00, 1500.00Diameter / µm16.38Membrane / mVRun experimentOutward current / nA—

Contact placement · conservative membrane-clearance estimates (µm)
Contact / role	Depth Z	Soma	Axon	Selected	Nearest membrane
r4-c4 Recording	1500.00	83.69	74.27	83.69	36.20 dend[3]:2
r4-c5 Recording	1500.00	283.69	307.63	283.69	129.54 dend[29]:4

Selected contacts pass the 25 µm numerical exclusion. This does not validate near-field accuracy or mechanical clearance.

4 / Replay & inspect

01 → 02 → 03

Membrane equations → transmembrane currents → contact potentials.

No synthetic recording templates are used in this experiment.

Model limits & next steps

This model has reconstructed human temporal-cortex dendrites, fitted active channels and a short synthetic axon stub. It does not reconstruct a full projection axon or establish M1/S1 excitability. Computed threshold crossings depend on this cell, the stub, placement and numerical refinement. Coupled population activity, layered conductivity, finite exposed contacts, acquisition electronics, mechanics and independent experimental validation remain outside this milestone.

The existing active stimulation and synthetic recording tools remain available under Simulations. Their outputs are not validation of this model.

Read the scientific scope →

cortex-active/0.2.0

Finite disk stimulation benchmark — reconstructed human cell, membrane replay, source and validation.