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Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids.

Code ↔ Paper

5 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 5 matches · 3 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Data processing of Ca2+ imaging dataset ↔ Matlab/Graph/matlab_bgl/fruchterman_reingold_force_directed_layout.m, the whole file · a weak match · score 0.83 · Fruchterman Reingold, force directed, Kamada Kawai, undirected graph, MATLAB, positions
  2. [2] § Methods › Data processing of Ca2+ imaging dataset ↔ Matlab/Graph/code/+graph/FRKK.m, lines 1–112 · score 0.80 · Fruchterman Reingold algorithm, Kamada Kawai algorithm, adjacency matrix, force, nodes, network
  3. [3] § Methods › Data processing of Ca2+ imaging dataset › Small-world propensity ↔ Matlab/Graph/code/+graph/small_world_propensity.m, lines 1–117 · score 0.66 · fractional deviation, random network, propensity, SWP, coefficient, clustering
  4. [4] § Methods › Three-photon and two-photon microscope for calcium imaging ↔ Matlab/+Package/suite2p-main/helpers/make_json_config.m, the whole file · a weak match · score 0.57 · ScanImage, frame rate, resolution, scanned, fs
  5. [5] § Methods › Three-photon and two-photon microscope for calcium imaging ↔ Matlab/+Package/suite2p-main/suite2p/default_ops.py, the whole file · a weak match · score 0.51 · pass filter, ScanImage, scanned, fs, photon, frame

Paper

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The authors' code

MATLAB · 65 lines · 2.5 KB · no license · 1 match

  1. function X = fruchterman_reingold_force_directed_layout(A,varargin)
  2. % FRUCHTERMAN_REINGOLD_FORCE_DIRECTED_LAYOUT A force directed graph layout
  3. %
  4. % Compute the layout for an unweighted, undirected graph.
  5. % See
  6. % http://www.boost.org/doc/libs/1_36_0/libs/graph/doc/fruchterman_reingold.html
  7. % for information about the layout function and the parameters
  8. %
  9. % The temperature of the layout begins at the value initial_temp and
  10. % decreases to 0 over the number of iterations given.
  11. %
  12. % ... = fruchterman_reingold_force_directed_layout(A,...) takes a set of
  13. % key-value pairs or an options structure. See set_matlab_bgl_options
  14. % for the standard options.
  15. % options.iterations: number of layout iterations [int > 0 | {100}]
  16. % options.initial_temp: starting temperature [double > 0 | {10}]
  17. % options.force_pairs: computation of forces between pairs of vertices can
  18. % either be approximated on a grid or computed between all pairs
  19. % [{'grid'} | 'all']
  20. % options.width: width of layout area [double | {num_vertices(G)}]
  21. % options.height: height of layout area [double | {num_vertices(G)}]
  22. % options.progressive: whether to start from an old layout
  23. % [{0} | position matrix X]
  24. %
  25. % Note: this function does not depend on the non-zero values of A,
  26. % but only uses the non-zero structure of A
  27. %
  28. % Example:
  29. % G = grid_graph(6,5);
  30. % X = fruchterman_reingold_force_directed_layout(G);
  31. % gplot(G,X);
  32. % X = fruchterman_reingold_force_directed_layout(G,'initial_temp',100);
  33. %
  34. % See also KAMADA_KAWAI_SPRING_LAYOUT, GURSOY_ATUN_LAYOUT, LAYOUT
  36. % David F. Gleich
  37. % Copyright, Stanford University, 2008
  39. %% History
  40. % 2008-09-25: Initial coding
  41. %%
  43. [trans check full2sparse] = get_matlab_bgl_options(varargin{:});
  44. if full2sparse && ~issparse(A), A = sparse(A); end
  46. n = num_vertices(A);
  47. options = struct('iterations',100,'initial_temp',10,'force_pairs','grid',...
  48. 'width',n,'height',n,'progressive',0);
  49. options = merge_options(options,varargin{:});
  51. if check, check_matlab_bgl(A,struct('sym',1)); end
  53. progressive_opt = [];
  54. if ~isscalar(options.progressive), progressive_opt = options.progressive; end
  56. force_pair_type = 0;
  57. switch options.force_pairs
  58. case 'grid', force_pair_type = 1;
  59. case 'all', force_pair_type = 0;
  60. otherwise, error('matlab_bgl:invalidParameter',...
  61. 'force_pair = %s isn''t a recognized option',options.force_pair);
  62. end
  64. X = fruchterman_reingold_mex(A,options.iterations,options.initial_temp,...
  65. force_pair_type, options.width, options.height, progressive_opt);

fruchterman_reingold_force_directed_layout.m at commit 67ec054, no license · at the source

Overview

Authors: Tatsuya Osaki1,2, Chloe Delepine1, Yuma Osako1, Devorah Kranz3,4, April Levin5,6, Charles Nelson3,4,7, Michela Fagiolini6,8,9, Mriganka Sur1,10
ORCID iDs: Tatsuya Osaki, Chloe Delepine, Yuma Osako, Devorah Kranz, Charles Nelson, Michela Fagiolini, Mriganka Sur
  1. Picower Institute for Learning and Memory, Massachusetts Institute of Technology,Cambridge, MA USA
  2. Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology,Cambridge, MA USA
  3. Division of Developmental Medicine, Boston Children’s Hospital,Boston, MA USA
  4. Department of Pediatrics, Harvard Medical School,Cambridge, MA USA
  5. Graduate School of Education, Harvard University,Boston, MA USA
  6. F.M. Kirby Neurobiology Division, Boston Children’s Hospital,Boston, MA USA
  7. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology,Cambridge, MA USA
  8. Department of Neurology, Boston Children’s Hospital,Boston, MA USA
  9. Harvard Medical School,Boston, MA USA
  10. International Research Center for Neurointelligence, The University of Tokyo, Institutes for Advanced Study,Tokyo, Japan
Institutions: Massachusetts Institute of Technology (United States); Boston Children's Hospital (United States); Harvard University (United States); The University of Tokyo (Japan)
Journal: Nature communications, volume 17, issue 1, article 5225
Dates: received 16 September 2024; accepted 17 March 2026; published online 14 April 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-71458-0 · PMID 41980938 · PMCID PMC13260836 · OpenAlex W7154364422
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), other condition (population), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Preprocessing, Connectivity, Statistics, Smoothing, state filtering, decompositions, Evoked potentials, Graphs, Machine learning, fMRI & imaging, Single-unit activity, calcium imaging
Keywords: Cellular neuroscience, Stem cells in the nervous system
MeSH: Cerebral Cortex*, Methyl-CpG-Binding Protein 2*, Mutation*, Organoids*, Rett Syndrome*, Female, Histone Deacetylase 2, Humans, Induced Pluripotent Stem Cells, Mutation, Missense, Neurons, Receptors, GABA-A (* major topic)
Topic: Genetics and Neurodevelopmental Disorders (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Institute of Mental Health (R01MH085802)
Citations: cited by 1 paper (Europe PMC); 67 references in the paper
Research resources: RRID:Addgene_100854, RRID:Addgene_83900

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 5 matches between paragraphs and lines of code.

TatsuyaOsaki/network-analysis-organoid-imaging

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 67ec054d6a0552e28a74e9c3323590a91b5515ec, 1 March 2026
Languages: MATLAB (491), Python (77), C++ (24), C (24), C/C++ (7), Shell (6), Jupyter (4), Java (1)
Size: 1,144 files, 634 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, environment (Matlab/+Package/suite2p-main/environment.yml, Matlab/+Package/suite2p-main/setup.cfg, Matlab/+Package/suite2p-main/setup.py), tests, documentation, 8 notebooks
Not found: license file, CITATION.cff, continuous integration
Tools: NumPy (59 files), Image Processing Toolbox (46 files), Statistics and Machine Learning Toolbox (27 files), SciPy (23 files), Parallel Computing Toolbox (17 files), Signal Processing Toolbox (17 files), Suite2p (17 files), Matplotlib (6 files), Numba (5 files), tifffile (5 files), Optimization Toolbox (4 files), Brain Connectivity Toolbox (3 files), Wavelet Toolbox (3 files), OpenCV (3 files), PyTorch (3 files), scikit-learn (3 files), Cellpose (2 files), Neurodata Without Borders (PyNWB, MatNWB) (2 files), scikit-image (2 files), cowplot (1 file), edgeR (1 file), h5py (1 file), limma (1 file), Deep Learning Toolbox (1 file), patchwork (1 file), pheatmap (1 file), reshape2 (1 file), Seurat (1 file), SingleCellExperiment (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
632 files
At the source: github.com/TatsuyaOsaki/network-analysis-organoid-imaging

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41467-026-71458-0.

Tracing map

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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;
  • 632 scripts, each with its path and the digest of its content;
  • 5 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41467-026-71458-0.

Versions

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 2 keywords, 12 MeSH terms, 1 funder, 67 references, 2 RRIDs.

Cite

This paper

Osaki, T., Delepine, C., Osako, Y., Kranz, D., Levin, A., Nelson, C., Fagiolini, M., & Sur, M. (2026). Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids. Nature communications, 17(1), 5225. https://doi.org/10.1038/s41467-026-71458-0

BibTeX

@article{osaki2026early,
author = {Osaki, Tatsuya and Delepine, Chloe and Osako, Yuma and Kranz, Devorah and Levin, April and Nelson, Charles and Fagiolini, Michela and Sur, Mriganka},
title = {{Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids}},
journal = {Nature communications},
year = {2026},
month = apr,
volume = {17},
number = {1},
pages = {5225},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-71458-0},
url = {https://doi.org/10.1038/s41467-026-71458-0},
pmid = {41980938},
pmcid = {PMC13260836}
}

RIS

TY - JOUR
AU - Osaki, Tatsuya
AU - Delepine, Chloe
AU - Osako, Yuma
AU - Kranz, Devorah
AU - Levin, April
AU - Nelson, Charles
AU - Fagiolini, Michela
AU - Sur, Mriganka
TI - Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/04/14
VL - 17
IS - 1
SP - 5225
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-71458-0
UR - https://doi.org/10.1038/s41467-026-71458-0
LA - en
ER -

CSL-JSON

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"issued": {
"date-parts": [
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14
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]
}
}

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