OSCR

Sometimes extracellular recordings fail for good reasons.

Code ↔ Paper

12 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 12 matches · 6 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Cable equation representation of a simplified neuron ↔ EP_code/NeuronCable/run_simulation.m, the whole file · a weak match · score 0.88 · simplified neuron, membrane capacitance, intracellular conductivity, neuron model, extracellular conductivity, extracellular potential
  2. [2] § Methods › Bidomain model representation of a sinoatrial node tissue sample ↔ EP_code/Heart-on-a-chip/model_parameters.m, the whole file · a weak match · score 0.85 · volume fraction, gap junction, membrane capacitance, extracellular space, model parameters, Gg
  3. [3] § Methods › Bidomain model representation of a sinoatrial node tissue sample ↔ EP_code/SAN/run_simulation.m, lines 1–42 · score 0.84 · sinoatrial node, tissue sample, bidomain model parameters, extracellular bath, lz, lx
  4. [4] § Methods › KNM representation of a heart-on-a-chip ↔ EP_code/Heart-on-a-chip/model_parameters.m, the whole file · a weak match · score 0.80 · volume fraction, gap junction, membrane capacitance, extracellular space, Gg, lz
  5. [5] § Methods › Bidomain model representation of a sinoatrial node tissue sample ↔ EP_code/SAN/run_simulation.m, lines 1–42 · score 0.75 · sinoatrial node tissue, extracellular bath, bidomain model
  6. [6] § Methods › KNM representation of a heart-on-a-chip ↔ EP_code/Heart-on-a-chip/run_simulation.m, the whole file · a weak match · score 0.70 · gap junction conductance, hiPSC, chip, Gg, CMs, lx
  7. [7] § Methods › KNM representation of a pancreatic islet ↔ EP_code/SAN/model_parameters.m, the whole file · a weak match · score 0.69 · volume fraction, gap junction, membrane model, lz, lx, ly
  8. [8] § Methods › Cable equation representation of a simplified neuron › Numerical methods ↔ EP_code/NeuronCable/run_simulation.m, the whole file · a weak match · score 0.67 · ode15s, simplified neuron, solver, compartments, cable, discretized
  9. [9] § Methods › EMI model representation of a cerebellar Purkinje neuron ↔ EP_code/Purkinje/EMI_one_cell.cpp, lines 1–19 · score 0.52 · cerebellar Purkinje neuron, EMI model, membrane
  10. [10] § Methods › EMI model representation of a cerebellar Purkinje neuron ↔ EP_code/Purkinje/EMI_two_cells.cpp, lines 1–19 · score 0.52 · cerebellar Purkinje neuron, EMI model, membrane
  11. [11] § Methods › EMI model representation of a cerebellar Purkinje neuron › Numerical methods ↔ EP_code/Purkinje/EMI_one_cell.cpp, lines 1–19 · score 0.50 · finite element, EMI model, MFEM, space, membrane
  12. [12] § Methods › EMI model representation of a cerebellar Purkinje neuron › Numerical methods ↔ EP_code/Purkinje/Masoli2015.h, lines 677–728 · score 0.50 · Rush Larsen algorithm

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

MATLAB · 101 lines · 2.8 KB · CC-BY-4.0 · 2 matches

  1. % Run a simulation of a simplified neuron modeled by the cable equation
  2. clear all
  4. % Specify simulation options
  5. Na_move_percentage = 10;
  6. use_stim = 0;
  8. % Set up cable equation parameters
  9. Tstop = 10000; % Total simulation time (in ms)
  10. L = 1000e-4; % Cell length (in cm)
  11. d = 10e-4; % Cell diameter (in cm)
  12. sigma_i = 8.2; % Intracellular conductivity (in mS/cm)
  13. sigma_e = 3; % Extracellular conductivity (in mS/cm)
  14. Cm = 1; % Specific membrane capacitanceuF/cm^2
  15. N = 1000; % Number of discrete compartments
  16. dx = L/N; % Length of each compartment (in cm)
  17. eta = d*sigma_i/4;
  19. % Set up membrane model parameters
  20. [param, param_names] = Masoli2015_init_parameters();
  21. Np = length(param);
  22. param = repmat(param, N, 1);
  24. % Adjust g_Na
  25. idx = round(N/2);
  26. gNa_idx = find(strcmp(param_names, 'g_Na'));
  27. gNa_bar = param(gNa_idx);
  28. gNa_small = (1 - Na_move_percentage/100)*gNa_bar;
  29. gNa_large = gNa_small + (Na_move_percentage/100)*(100/4)*gNa_bar;
  30. param((0:N-1)*Np + gNa_idx) = gNa_small;
  31. param((idx-20:idx+19)*Np + gNa_idx) = gNa_large;
  33. % Set up stimulation
  34. if use_stim
  35. stim_idx = find(strcmp(param_names, 'stim_amplitude'));
  36. stim_start_idx = find(strcmp(param_names, 'stim_start'));
  37. param((0:N-1)*Np + stim_start_idx) = 1;
  38. param((idx-1)*Np + stim_idx) = 3;
  39. param((idx)*Np + stim_idx) = 3;
  40. param((idx-2)*Np + stim_idx) = 3;
  41. param((idx+1)*Np + stim_idx) = 3;
  42. end
  44. % Set up initial conditions
  45. [states, state_names] = Masoli2015_init_states();
  46. Ns = length(states);
  47. V_idx = find(strcmp(state_names, 'v'));
  48. states = repmat(states, N, 1);
  50. % Set up G matrix
  51. G = spdiags([-1; -2*ones(N-2,1); -1], 0, N, N);
  52. G = G + spdiags(ones(N, 1), 1, N, N);
  53. G = G + spdiags(ones(N, 1), -1, N, N);
  54. G = G*eta/(Cm*dx^2);
  56. % Set up solver options
  57. S_pattern = set_up_sparsity_pattern(N, Ns, V_idx);
  58. if use_stim
  59. options = odeset('JPattern', S_pattern, 'MaxStep', 0.01);
  60. else
  61. options = odeset('JPattern', S_pattern);
  62. end
  64. % Perform a cable model simulation
  65. P.parameters = param; P.N = N; P.G = G;
  66. [T, S] = ode15s(@system_rhs, [0, Tstop], states, options, P);
  67. V = S(:, V_idx:Ns:end);
  69. % Extract the current sources for comuputing the extracellular potential
  70. Im = G*V'; % Transmenbrane current density
  71. c = (dx*d*pi)*Im; % Current source
  73. % Set up spatial points for computing the extracellular potential
  74. x = (dx/2:dx:L-dx/2);
  75. z = zeros(N, 1);
  76. y_cell = zeros(N, 1);
  77. y_e = 6e-4*ones(N, 1);
  79. % Compute the extracellular potential
  80. ue = zeros(N, length(T));
  81. for n=1:N
  82. for k=1:N
  83. ue(n,:) = ue(n,:) + (1/(4*pi*sigma_e))*c(k,:)/(norm([x(n);y_e(n);z(n)]-[x(k);y_cell(k);z(k)]));
  84. end
  85. end
  88. % Plot the membrane potential and the extracellular potential in two points
  89. plot_idx = [idx + 1, idx + round(N/6)];
  90. subplot(2,1,1)
  91. plot(T, V(:, plot_idx), 'LineWidth', 2);
  92. ylabel('v (mV)')
  94. subplot(2,1,2)
  95. plot(T, ue(plot_idx,:), 'LineWidth', 2);
  96. ylabel('u_e (\muV)')
  97. xlabel('t (ms)')

run_simulation.m, under CC-BY-4.0 · at the source

Overview

Authors: Karoline Horgmo Jæger1, Aslak Tveito1
  1. Simula Research Laboratory,Oslo, Norway
Institutions: Simula Research Laboratory (Norway)
Journal: NPJ systems biology and applications, volume 12, issue 1, article 101
Dates: received 4 August 2025; accepted 20 April 2026; published online 2 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41540-026-00730-2 · PMID 42069702 · PMCID PMC13342592 · OpenAlex W7159954052
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: EEG (modality), other (modality), extracellular electrophysiology (units, LFP) (modality), human (organism), cellular / molecular (subfield)
Methods: Smoothing, state filtering, decompositions
Keywords: Biological techniques, Cell biology, Engineering, Neuroscience, Stem cells
MeSH: Action Potentials*, Electrocardiography*, Electroencephalography*, Animals, Humans, Induced Pluripotent Stem Cells, Insulin-Secreting Cells, Myocytes, Cardiac, Neurons, Purkinje Cells, Sodium Channels (* major topic)
Topic: Cardiac electrophysiology and arrhythmias (Cardiology and Cardiovascular Medicine, Medicine), according to OpenAlex
Funding: Norges Forskningsråd (Forskningsrådet) (355113)
Citations: cited by 1 paper (Europe PMC); 70 references in the paper

Abstract

Excitable cells are commonly studied via the extracellular potentials (EPs) they generate, which underlie signals in electroencephalography (EEG), electrocardiography (ECG), and multielectrode array (MEA) recordings. However, some excitable systems produce little or no detectable EPs, for reasons that remain poorly understood. Here we show mathematically that homogeneous excitable cells and tissues – with spatially uniform ion channel distributions and no external stimulation – are extracellularly silent during spatially uniform, non-propagating action potentials (i.e., in the absence of a traveling wavefront). Specifically, an isolated, autonomous cell with uniform membrane properties generates zero EP, independent of shape, kinetics, or model complexity. The result extends to coupled cells provided the tissue remains fully homogeneous. EPs emerge only from spatial inhomogeneities, propagating electrical waves, or applied currents. We demonstrate the physiological relevance of this principle in Purkinje neurons, where clustering of sodium channels enables ephaptic synchronization, while uniform cells remain asynchronous and undetectable extracellularly. We further show that connected human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and pancreatic β-cells exhibit EPs in proportion to cellular or tissue-level heterogeneity.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 12 matches between paragraphs and lines of code.

Zenodo 18198916

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
41 files
At the source:

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 41 scripts, each with its path and the digest of its content;
  • 12 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

The data and code generated in this study are publicly available at Zenodo: 10.5281/zenodo.18198916.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 5 keywords, 11 MeSH terms, 1 funder, 63 references.

Cite

This paper

Jæger, K. H., & Tveito, A. (2026). Sometimes extracellular recordings fail for good reasons. NPJ systems biology and applications, 12(1), 101. https://doi.org/10.1038/s41540-026-00730-2

BibTeX

@article{jger2026sometimes,
author = {Jæger, Karoline Horgmo and Tveito, Aslak},
title = {{Sometimes extracellular recordings fail for good reasons}},
journal = {NPJ systems biology and applications},
year = {2026},
month = may,
volume = {12},
number = {1},
pages = {101},
publisher = {Nature Publishing Group},
issn = {2056-7189},
doi = {10.1038/s41540-026-00730-2},
url = {https://doi.org/10.1038/s41540-026-00730-2},
pmid = {42069702},
pmcid = {PMC13342592}
}

RIS

TY - JOUR
AU - Jæger, Karoline Horgmo
AU - Tveito, Aslak
TI - Sometimes extracellular recordings fail for good reasons
T2 - NPJ systems biology and applications
J2 - NPJ Syst Biol Appl
PY - 2026
DA - 2026/05/02
VL - 12
IS - 1
SP - 101
SN - 2056-7189
PB - Nature Publishing Group
DO - 10.1038/s41540-026-00730-2
UR - https://doi.org/10.1038/s41540-026-00730-2
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41540-026-00730-2",
"type": "article-journal",
"title": "Sometimes extracellular recordings fail for good reasons",
"container-title": "NPJ systems biology and applications",
"author": [
{
"family": "Jæger",
"given": "Karoline Horgmo"
},
{
"family": "Tveito",
"given": "Aslak"
}
],
"container-title-short": "NPJ Syst Biol Appl",
"volume": "12",
"issue": "1",
"page": "101",
"DOI": "10.1038/s41540-026-00730-2",
"PMID": "42069702",
"PMCID": "PMC13342592",
"ISSN": "2056-7189",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41540-026-00730-2",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
2
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.7554/elife.103046 [code]
Dichotomy between extracellular signatures of active dendritic chemical synapses and gap junctions.
Journal: eLife
In common: extracellular electrophysiology (units, LFP), cellular / molecular, 3 references
[2] doi:10.1523/jneurosci.1594-25.2026 [code]
KIASORT: Knowledge-Integrated Automated Spike Sorting for Geometry-Free Neuron Tracking.
Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience
In common: extracellular electrophysiology (units, LFP), 2 references
[3] doi:10.7554/elife.110013 [code]
Large-scale synthetic data enable digital twins of human excitable cells.
Journal: eLife
In common: cellular / molecular, 2 references
[4] doi:10.1371/journal.pone.0333158 [code]
Alpha-synuclein overexpression reduces neural activity within a basal ganglia vocal nucleus in a zebra finch model.
Journal: PloS one
In common: cellular / molecular, 2 references
[5] doi:10.1038/s41598-026-46512-y [code]
Glucose-driven intra- and inter-islet beta cell synchronization in pancreatic tissue slices.
Journal: Scientific reports
In common: cellular / molecular, 2 references
[6] doi:10.1038/s41467-026-75826-8
Transcranial focused ultrasound modulates spiking, LFP, and BOLD activity in the primate thalamus.
Journal: Nature communications
In common: extracellular electrophysiology (units, LFP), other, 1 reference
[7] doi:10.1016/j.celrep.2026.117420 [code]
Neural population dynamics of direct electrical stimulation of neocortex.
Journal: Cell reports
In common: extracellular electrophysiology (units, LFP), 1 reference
[8] doi:10.7554/elife.110170 [code]
Efficient and reproducible pipelines for spike sorting large-scale electrophysiology data.
Journal: eLife
In common: extracellular electrophysiology (units, LFP), 1 reference
[9] doi:10.1002/advs.202519893 [code]
NeuroSuite for Long-Term Functional and Structural Studies of Air-Liquid Interface Cerebral Organoids.
Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)
In common: extracellular electrophysiology (units, LFP), 1 reference
[10] doi:10.3390/biology15131074
The Distinct Electrophysiological Mechanisms in the Cortico-Striatal Circuit of LID Rats.
Journal: Biology
In common: extracellular electrophysiology (units, LFP), 1 reference

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.