OSCR

NeuroSuite for Long-Term Functional and Structural Studies of Air-Liquid Interface Cerebral Organoids.

Code ↔ Paper

11 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 11 matches · 7 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and Methods › Data Pre‐Processing–Quality Assessment ↔ GUI Files/gui_plot_functions/Frequency Plots/update_power_spectrum_tab.m, lines 108–193 · score 0.65 · Power spectral density, Welch, noisy, Hz, PSD, STD
  2. [2] § Materials and Methods › Data Pre‐Processing–Referencing and Filtering ↔ GUI Files/gui_callback_functions/LFP Analysis/PAC_callback.m, the whole file · a weak match · score 0.64 · high gamma, eegfilt, band, beta, theta, alpha
  3. [3] § Materials and Methods › Data Pre‐Processing–Quality Assessment ↔ GUI Files/gui_plot_functions/Frequency Plots/plot_power_spectrum.m, the whole file · a weak match · score 0.64 · Power spectral density, Welch, noisy, Hz, PSD, STD
  4. [4] § Materials and Methods › Local‐Field Potential (LFP) Analysis–Oscillatory Analysis ↔ GUI Files/gui_plot_functions/Frequency Plots/plot_power_spectrum.m, the whole file · a weak match · score 0.63 · power spectral densities, Welch, PSDs
  5. [5] § Materials and Methods › Local‐Field Potential (LFP) Analysis–Oscillatory Analysis ↔ GUI Files/gui_plot_functions/Frequency Plots/update_power_spectrum_tab.m, lines 108–193 · score 0.63 · power spectral densities, Welch, PSDs
  6. [6] § Materials and Methods › MUA Analysis–Spike Sorting and Clustering ↔ GUI Files/gui_callback_functions/Clustering/clusters_callback.m, the whole file · a weak match · score 0.62 · principal components, GMM, centroids, cluster, score, PCA
  7. [7] § Materials and Methods › LFP Analysis–Continuous Wavelet Transform (CWT) ↔ GUI Files/gui_util_funcs/applyFilters.m, lines 112–190 · score 0.60 · wavelet transform, low pass filtered, CWT, LFP, signal
  8. [8] § Results › NeuroSuite Reveals Age‐Dependent Shifts in Low‐Frequency Network Dynamics ↔ GUI Files/gui_plot_functions/LFP Features/plot_exp_callback.m, the whole file · a weak match · score 0.55 · aperiodic offset, Power spectral density, exponent, fits, LFPs, 40 Hz
  9. [9] § Materials and Methods › Data Pre‐Processing–Referencing and Filtering ↔ GUI Files/gui_util_funcs/applyFilters.m, lines 27–110 · score 0.54 · powerline filtered, bandwidth, 400 Hz, channels, 50 kHz, 100 Hz
  10. [10] § Materials and Methods › MUA Analysis–Spike Sorting and Clustering ↔ GUI Files/gui_callback_functions/Clustering/clusters_callback.m, the whole file · a weak match · score 0.52 · principal component, clustering, score, PCA, waveform, Spike
  11. [11] § Materials and Methods › Local‐Field Potential (LFP) Analysis–Oscillatory Analysis ↔ GUI Files/gui_plot_functions/LFP Features/plot_exp_callback.m, the whole file · a weak match · score 0.51 · aperiodic exponent, FOOOF, offset, fit, LFP, power

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 · 193 lines · 6.5 KB · MIT · 2 matches

  1. function update_power_spectrum_tab(h)
  2. h=guidata(h.figure);
  3. % Get selection
  4. set_status(h.figure,"loading","Computing Power Spectrum...");
  5. if isfield(h,'pspec_props')
  6. p = h.pspec_props;
  7. else
  8. p.fmin = 1;
  9. p.fmax = [];
  10. p.xscale = 'log';
  11. p.yscale = 'log';
  12. p.showWelch = true;
  13. p.linewidth = 1.5;
  14. p.winLen = 2; %seconds
  15. p.stepLen = 0.5; %seconds
  16. end
  17. idx = h.portList.Value;
  18. map = h.portList.UserData;
  19. selected = map(idx,:);
  20. exclude_impedance_chans_toggle = get(h.excl_imp_toggle,'Value');
  21. exclude_noisy_chans_toggle = get(h.excl_high_STD_toggle,'Value');
  22. selectedObj = h.formatToggleGroup.SelectedObject;
  23. if isempty(selectedObj) || ~isvalid(selectedObj) || ~isprop(selectedObj, 'String')
  24. selectedStr = 'Raw';
  25. else
  26. selectedStr = selectedObj.String;
  27. end
  28. lab = extract_lab(selectedStr);
  29. legendStrings = {};
  30. % Global mode or multiple ports
  31. if h.pspec_toggle.Value || (size(selected,1) > 1 && h.pspec_toggle.Value)
  32. axes(h.psAxes); hold(h.psAxes,'on');
  33. colors = lines(size(selected,1));
  34. for selIdx = 1:size(selected,1)
  35. expIdx = selected(selIdx,1);
  36. port_idx = selected(selIdx,2);
  37. if iscell(h.figure.UserData)
  38. results = h.figure.UserData{expIdx};
  39. else
  40. results = h.figure.UserData;
  41. end
  42. % Mask channels
  43. channels = results.channels(port_idx).id;
  44. mask = true(1,numel(channels));
  45. if exclude_impedance_chans_toggle
  46. mask = mask & ~results.channels(port_idx).bad_impedance;
  47. end
  48. if exclude_noisy_chans_toggle
  49. noisy = results.channels(port_idx).high_psd & results.channels(port_idx).high_std;
  50. mask = mask & ~noisy;
  51. end
  52. channels = channels(mask);
  53. signals = results.signals(port_idx).(lab)(mask,:);
  54. fs = results.fs;
  55. win_samples = round(fs*p.winLen);
  56. stepLen = round(fs*p.stepLen);
  57. Nfft = win_samples;
  58. f_axis = linspace(0, fs/2, floor(Nfft/2)+1);
  59. goodMask = any(signals,2);
  60. PSDm = mPSD(signals(goodMask,:), round(fs), win_samples, stepLen, stepLen);
  61. set_status(h.figure,"loading","Plotting Power Spectrum...");
  62. if isfield(h,'psLines') && all(isvalid(h.psLines))
  63. set(h.psLines, 'XData', nan, 'YData', nan);
  64. end
  65. if isfield(h,'psLinesWelch') && all(isvalid(h.psLinesWelch))
  66. set(h.psLinesWelch, 'XData', nan, 'YData', nan);
  67. end
  68. % Update pre-created line or create temp line if needed
  69. if selIdx <= numel(h.psLines)
  70. set(h.psLines(selIdx), 'XData', f_axis, 'YData', mean(PSDm,2)', 'Color', colors(selIdx,:), 'LineWidth',p.linewidth);
  71. else
  72. loglog(h.psAxes, f_axis, mean(PSDm,2)', 'Color', colors(selIdx,:), 'LineWidth',p.linewidth);
  73. end
  74. legendStrings{end+1} = sprintf('Exp %d Port %d %s', expIdx, results.ports(port_idx).port_id, [upper(lab(1)) lower(lab(2:end))]);
  75. end
  76. if isempty(p.fmax)
  77. p.fmax = fs/2;
  78. end
  79. xlim(h.psAxes,[p.fmin p.fmax])
  80. set(h.psAxes,'XScale',p.xscale,'YScale',p.yscale);
  81. title('');
  82. else
  83. % Single-channel mode
  84. expIdx = selected(1,1);
  85. port_idx = selected(1,2);
  86. if iscell(h.figure.UserData)
  87. results = h.figure.UserData{expIdx};
  88. else
  89. results = h.figure.UserData;
  90. end
  91. % Mask channels
  92. channels = results.channels(port_idx).id;
  93. mask = true(1,numel(channels));
  94. if exclude_impedance_chans_toggle
  95. mask = mask & ~results.channels(port_idx).bad_impedance;
  96. end
  97. if exclude_noisy_chans_toggle
  98. noisy = results.channels(port_idx).high_psd & results.channels(port_idx).high_std;
  99. mask = mask & ~noisy;
  100. end
  101. channels = channels(mask);
  102. signals = results.signals(port_idx).(lab)(mask,:);
  103. SeriesNumber = round(get(h.series_slider,'Value'));
  104. sig = signals(SeriesNumber,:)';
  105. fs = results.fs;
  106. win_samples = round(fs*p.winLen);
  107. stepLen = round(fs*p.stepLen);
  108. Nfft = win_samples; % or as used in mPSD
  109. f_axis = linspace(0, fs/2, floor(Nfft/2)+1);
  110. if ~isfield(h,'psdCache') || ...
  111. h.psdCache.expIdx ~= expIdx || ...
  112. h.psdCache.port_idx ~= port_idx || ...
  113. h.psdCache.SeriesNumber ~= SeriesNumber || ...
  114. ~strcmp(h.psdCache.lab, lab)
  115. % compute PSD
  116. PSDm = mPSD(sig', round(fs), win_samples, stepLen, stepLen);
  117. PSDw = pwelch(sig, win_samples, round(fs), win_samples, round(fs));
  118. % store in cache
  119. h.psdCache.expIdx = expIdx;
  120. h.psdCache.port_idx = port_idx;
  121. h.psdCache.SeriesNumber = SeriesNumber;
  122. h.psdCache.lab = lab;
  123. h.psdCache.PSDm = PSDm;
  124. h.psdCache.PSDw = PSDw;
  125. end
  126. % use cached PSDs for plotting
  127. PSDm = h.psdCache.PSDm;
  128. PSDw = h.psdCache.PSDw;
  129. set_status(h.figure,"loading","Plotting Power Spectrum...");
  130. if isfield(h,'psLines') && all(isvalid(h.psLines))
  131. set(h.psLines, 'XData', nan, 'YData', nan);
  132. end
  133. if isfield(h,'psLinesWelch') && all(isvalid(h.psLinesWelch))
  134. set(h.psLinesWelch, 'XData', nan, 'YData', nan);
  135. end
  136. if p.showWelch
  137. set(h.psLinesWelch, 'XData', f_axis, 'YData', PSDw,'DisplayName', 'Welch_PSD');
  138. else
  139. set(h.psLinesWelch, 'XData', nan, 'YData', nan);
  140. end
  141. % Update pre-created lines
  142. set(h.psLines(1), 'XData', f_axis, 'YData', PSDm, 'Color','b', 'LineWidth',p.linewidth);
  143. if isempty(p.fmax)
  144. p.fmax = fs/2;
  145. end
  146. xlim(h.psAxes,[p.fmin p.fmax])
  147. legendStrings = {'Median PSD'};
  148. if p.showWelch
  149. legendStrings{end+1} = 'Welch PSD';
  150. end
  151. title(h.psAxes,sprintf('Port %d Ch %d %s', results.ports(port_idx).port_id,channels(SeriesNumber),[upper(lab(1)) lower(lab(2:end))]));
  152. end
  153. % Axis formatting
  154. set(h.psAxes,'XScale',p.xscale,'YScale',p.yscale);
  155. xlabel(h.psAxes,'Frequency (Hz)'); ylabel(h.psAxes,'Power Spectral Density (a.u.)');
  156. legend(h.psAxes, legendStrings,'Location','northeast');
  157. grid(h.psAxes,'on');
  158. tb_pspec = axtoolbar(h.psAxes,{'save','zoomin','zoomout','restoreview','pan'});
  159. axtoolbarbtn(tb_pspec, 'push', ...
  160. 'Icon','export_data_icon.png',...
  161. 'Tooltip', 'Export to CSV', ...
  162. 'ButtonPushedFcn', @(~,~) export_axes_to_csv(h.psAxes, 'power_spectrum'));
  163. drawnow limitrate;
  164. set_status(h.figure,"ready","Power Spectra Plot Complete...");
  165. guidata(h.figure,h);
  166. end

update_power_spectrum_tab.m at commit b115fae, under MIT · at the source

Overview

  1. Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
  2. MRC Laboratory of Molecular Biology, Cambridge, UK
  3. Institute for Biomedical Innovation, Department of Engineering, University of Cambridge, Cambridge, UK
  4. Division of Electrical Engineering, Department of Engineering, University of Cambridge, Cambridge, UK
  5. Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
Institutions: University of Cambridge (United Kingdom); MRC Laboratory of Molecular Biology (United Kingdom)
Dates: received 13 October 2025; accepted 25 July 2026; published online 6 August 2026; in print August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1002/advs.202519893 · PMID 42559667 · PMCID PMC13444802 · OpenAlex W4412872423
Open access: gold, a free copy (OpenAlex)
Status: code verified
Methods: Spectral & time-frequency, Preprocessing, Smoothing, state filtering, decompositions, Connectivity, Evoked potentials, Single-unit activity, calcium imaging
Keywords: air–liquid interface cultures, bioelectronics, brain organoids, electrophysiology, microelectrode arrays, multi‐unit analyses, neuronal interfaces
Topic: Neuroscience and Neural Engineering (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: Alzheimer's Research Trust (ARUK-PG013-14); Engineering and Physical Sciences Research Council (EP/L015978/1, EP/S022139/1, EP/L015889/1, G115857); Medical Research Council (MC_UP_1201/9, MR/K02292X/1); King's College, University of Cambridge; Arthritis UK (16238); Wellcome Trust (065807/Z/01/Z, 203249/Z/16/Z); Swiss National Science Foundation (P2EZP2_19984, P2EZP2_199843); Gates Cambridge Trust; Infinitus China Ltd; Michael J. Fox Foundation for Parkinson's Research (022159, 16238); Cambridge Trust; Michael J. Fox Foundation for Parkinson&apos;s Research (022159, 16238); Alzheimer&apos;s Research Trust (ARUK‐PG013‐14); Trinity College, University of Cambridge
Citations: not cited yet (Europe PMC); 80 references in the paper
Research resources: H9 RRID:CVCL_9773

Abstract

Long‐term electrophysiological monitoring of human cerebral organoids remains challenging, as 3D tissues rapidly develop necrotic cores once diffusion limits are exceeded. Air–liquid interface cerebral organoids (ALI‐COs) overcome this by maintaining thin slices with continuous metabolic exchange, preserving viability, yet no system allows stable, in situ recordings over months. Here, we introduce NeuroSuite, a modular platform for long‐term, spatially resolved neural monitoring of ALI‐COs. Its core, Neuroweb, is an ultrathin, perforated microelectrode array that preserves cellular diversity, evidenced by immunofluorescence and RNA sequencing, while enabling low‐impedance (∼25 kΩ at 1 kHz) recordings. Complementing this, NeuroMaps, our open‐source analysis suite, streamlines signal quality control, spike and field potential analysis, and integration with imaging. NeuroSuite is suitable for capturing maturation‐dependent network dynamics, including potential excitation‐inhibition shifts and oscillatory activity, beyond 180 days. Acute ex vivo rat brain slice recordings further demonstrate its versatility, establishing NeuroSuite as a robust platform for developmental neuroscience, disease modelling, and drug screening.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 11 matches between paragraphs and lines of code.

BelNeuroCoding/NeuroMaps

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: b115fae026575c600265790a589719e2af1d0c59, 22 June 2026
Languages: Python (4902), MATLAB (223), C/C++ (220), Fortran (61), C (60), JavaScript (16), Shell (3), C++ (2)
Size: 12,704 files, 5,487 scripts
Software Heritage: not checked
Found in: “Data Availability Statement”
Holds: README, tests, documentation
Not found: license file, CITATION.cff, environment file, continuous integration
Tools: NumPy (126 files), Matplotlib (105 files), specparam (formerly FOOOF) (67 files), Signal Processing Toolbox (17 files), Pillow (13 files), EEGLAB (10 files), Statistics and Machine Learning Toolbox (10 files), SciPy (4 files), Wavelet Toolbox (2 files), pandas (1 file), SymPy (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
1,713 files

madlancaster/Neuroweb

License: none: the authors keep all their rights
State: the link is dead, verified on 27 September 2026
Evidence: found in the paper
Software Heritage: not checked
Found in: “Data Availability Statement”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link is dead
  • 27 September 2026: the link is dead

Zenodo 19120269

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 12 files
Software Heritage: not checked
Found in: “Data Availability Statement”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
1 file
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:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1,712 scripts, each with its path and the digest of its content;
  • 11 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 Statement

The custom code for NeuroMaps is available on Github (https://github.com/BelNeuroCoding/NeuroMaps) and Zenodo (10.5281/zenodo.19120269). Code and data associated with bulk and scRNA‐seq analysis have are available on Github (https://github.com/madlancaster/Neuroweb). Further data is available from the corresponding author upon reasonable request.

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, 27 September 2026: the first record

Recorded: type, language, journal, pages, dates, 15 authors, 7 keywords, 14 funders, 74 references, 1 RRID.

Cite

This paper

Haider, B., Middya, S., Lloyd‐Davies‐Sánchez, D. J., Läubli, N. F., Vora, S., Träuble, J., Krajeski, R. N., Feng, Y., Duncko, D., Riley, J. S., Ruiz‐Mateos Serrano, R., Paulsen, O., Lancaster, M. A., Malliaras, G. G., & Kaminski Schierle, G. S. (2026). NeuroSuite for Long-Term Functional and Structural Studies of Air-Liquid Interface Cerebral Organoids. Advanced science (Weinheim, Baden-Wurttemberg, Germany), e19893. https://doi.org/10.1002/advs.202519893

BibTeX

@article{haider2026neurosuite,
author = {Haider, Belquis and Middya, Sagnik and Lloyd‐Davies‐Sánchez, Daniel J and Läubli, Nino F and Vora, Sulay and Träuble, Jakob and Krajeski, Rohan N and Feng, Yuqing and Duncko, Daniel and Riley, Josiah S and Ruiz‐Mateos Serrano, Rubén and Paulsen, Ole and Lancaster, Madeline A and Malliaras, George G and Kaminski Schierle, Gabriele S},
title = {{NeuroSuite for Long-Term Functional and Structural Studies of Air-Liquid Interface Cerebral Organoids}},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
year = {2026},
month = aug,
pages = {e19893},
publisher = {Wiley},
issn = {2198-3844},
doi = {10.1002/advs.202519893},
url = {https://doi.org/10.1002/advs.202519893},
pmid = {42559667},
pmcid = {PMC13444802}
}

RIS

TY - JOUR
AU - Haider, Belquis
AU - Middya, Sagnik
AU - Lloyd‐Davies‐Sánchez, Daniel J
AU - Läubli, Nino F
AU - Vora, Sulay
AU - Träuble, Jakob
AU - Krajeski, Rohan N
AU - Feng, Yuqing
AU - Duncko, Daniel
AU - Riley, Josiah S
AU - Ruiz‐Mateos Serrano, Rubén
AU - Paulsen, Ole
AU - Lancaster, Madeline A
AU - Malliaras, George G
AU - Kaminski Schierle, Gabriele S
TI - NeuroSuite for Long-Term Functional and Structural Studies of Air-Liquid Interface Cerebral Organoids
T2 - Advanced science (Weinheim, Baden-Wurttemberg, Germany)
J2 - Adv Sci (Weinh)
PY - 2026
DA - 2026/08/06
SP - e19893
SN - 2198-3844
PB - Wiley
DO - 10.1002/advs.202519893
UR - https://doi.org/10.1002/advs.202519893
LA - en
ER -

CSL-JSON

{
"id": "10.1002/advs.202519893",
"type": "article-journal",
"title": "NeuroSuite for Long-Term Functional and Structural Studies of Air-Liquid Interface Cerebral Organoids",
"container-title": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)",
"author": [
{
"family": "Haider",
"given": "Belquis"
},
{
"family": "Middya",
"given": "Sagnik"
},
{
"family": "Lloyd‐Davies‐Sánchez",
"given": "Daniel J"
},
{
"family": "Läubli",
"given": "Nino F"
},
{
"family": "Vora",
"given": "Sulay"
},
{
"family": "Träuble",
"given": "Jakob"
},
{
"family": "Krajeski",
"given": "Rohan N"
},
{
"family": "Feng",
"given": "Yuqing"
},
{
"family": "Duncko",
"given": "Daniel"
},
{
"family": "Riley",
"given": "Josiah S"
},
{
"family": "Ruiz‐Mateos Serrano",
"given": "Rubén"
},
{
"family": "Paulsen",
"given": "Ole"
},
{
"family": "Lancaster",
"given": "Madeline A"
},
{
"family": "Malliaras",
"given": "George G"
},
{
"family": "Kaminski Schierle",
"given": "Gabriele S"
}
],
"container-title-short": "Adv Sci (Weinh)",
"page": "e19893",
"DOI": "10.1002/advs.202519893",
"PMID": "42559667",
"PMCID": "PMC13444802",
"ISSN": "2198-3844",
"publisher": "Wiley",
"URL": "https://doi.org/10.1002/advs.202519893",
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
6
]
]
}
}

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