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Müller Glia-Vasculature Interactions in the Developing Retina.

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  1. [1] § Methods › Image Processing and Analysis: Calcium Imaging ↔ stalkEFpairs.m, lines 96 to 107 · score 0.57 · stalk endfoot pairs, calcium transients correlated, 1–2 s · Report a mismatch

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The authors' code

MATLAB · 134 lines · 3 KB · no license · 1 match

  1. %%% Stalk - endfoot pairs script
  3. %% Select CSV
  4. [file, path] = uigetfile('*.csv','Select peak CSV');
  6. if isequal(file,0)
  7. return
  8. end
  10. fullFile = fullfile(path,file);
  12. opts = delimitedTextImportOptions;
  14. opts.Delimiter = ',';
  15. opts.VariableNamesLine = 1;
  16. opts.DataLine = 2;
  17. opts.VariableNamingRule = 'preserve';
  19. T = readtable(fullFile, opts);
  21. %% Convert ROICorrelated to numeric
  22. T.ROICorrelated = str2double(string(T.ROICorrelated));
  24. disp(T.Properties.VariableNames')
  27. %% -----------------------------
  28. % Standardize category labels
  29. % Handles:
  30. % 'EF' or 'Endfoot'
  31. % 'Stalk'
  32. %% -----------------------------
  33. T.Category = string(T.Category);
  35. T.Category(ismember(lower(T.Category), ["ef", "endfoot"])) = "EF";
  36. T.Category(ismember(lower(T.Category), ["stalk"])) = "Stalk";
  38. %% -----------------------------
  39. % Unique experiments
  40. %% -----------------------------
  41. files = unique(T.FileName);
  43. % Preallocate
  44. EF_vals = nan(length(files),1);
  45. Stalk_vals = nan(length(files),1);
  47. %% -----------------------------
  48. % Compute % correlated per experiment
  49. %% -----------------------------
  50. for i = 1:length(files)
  52. idx_file = strcmp(T.FileName, files{i});
  53. subT = T(idx_file,:);
  55. % ----- Endfoot -----
  56. idx_ef = subT.Category == "EF";
  58. if any(idx_ef)
  59. EF_vals(i) = mean(subT.ROICorrelated(idx_ef), 'omitnan') * 100;
  60. end
  62. % ----- Stalk -----
  63. idx_stalk = subT.Category == "Stalk";
  65. if any(idx_stalk)
  66. Stalk_vals(i) = mean(subT.ROICorrelated(idx_stalk), 'omitnan') * 100;
  67. end
  69. end
  71. %% -----------------------------
  72. % Plot
  73. %% -----------------------------
  74. figure
  75. hold on
  77. jitterWidth = 0.15;
  79. xEF = centeredConditionalJitter(1, EF_vals, jitterWidth);
  80. xStalk = centeredConditionalJitter(2, Stalk_vals, jitterWidth);
  82. scatter(xEF, EF_vals, 90, 'filled')
  83. scatter(xStalk, Stalk_vals, 90, 'filled')
  85. % Connect paired experiments
  86. for i = 1:length(files)
  88. if ~isnan(EF_vals(i)) && ~isnan(Stalk_vals(i))
  89. plot([1 2], [EF_vals(i) Stalk_vals(i)], '-k')
  90. end
  92. end
  94. %% -----------------------------
  95. % Formatting
  96. %% -----------------------------
  97. xlim([0.5 2.5])
  98. ylim([0 100])
  100. xticks([1 2])
  101. xticklabels({'EF','Stalk'})
  103. ylabel('Proportion of calcium transients correlated with paired compartment')
  104. title('Correlation of Calcium Transients in Stalk-Endfoot Pairs')
  106. box off
  107. set(gca, 'FontSize', 12)
  109. %% =========================================================
  110. % Function for centered conditional jitter
  111. %% =========================================================
  112. function x_jittered = centeredConditionalJitter(x_base, y_vals, width)
  114. x_jittered = x_base * ones(size(y_vals));
  116. % Find unique Y values
  117. uniqueVals = unique(y_vals(~isnan(y_vals)));
  119. for k = 1:length(uniqueVals)
  121. idx = find(y_vals == uniqueVals(k));
  122. n = length(idx);
  124. if n > 1
  126. % Evenly spaced symmetric jitter
  127. offsets = linspace(-width/2, width/2, n);
  128. x_jittered(idx) = x_base + offsets;
  130. end
  132. end
  134. end

stalkEFpairs.m at commit 19c85d9, no license · at the source

Overview

Authors: Samira Monshietehadi1, Angel J. Garcia2, Benjamin E. Smith3, Matthew Tarchick1, Kiara Abhayaratne1, Aileen Conley3, Marla B. Feller1,2
  1. Department of Molecular and Cell Biology University of California, Berkeley Berkeley California USA
  2. Department of Neuroscience University of California, Berkeley Berkeley California USA
  3. School of Optometry, University of California, Berkeley Berkeley California USA
Institutions: University of California, Berkeley (United States)
Journal: Glia, volume 74, issue 10, article e70204
Dates: received 9 March 2026; accepted 10 July 2026; published online 4 August 2026; in print October 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1002/glia.70204 · PMID 42552727 · PMCID PMC13438127 · OpenAlex W7172526659
Open access: hybrid, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: optical imaging (calcium, voltage, 2-photon) (modality), mouse (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Preprocessing, fMRI & imaging, Single-unit activity, calcium imaging
Keywords: cholinergic activity, glial calcium dynamics, gliovascular interface, neuron–glia interactions, neurovascular development, neurovascular signaling, spontaneous network activity, vascular patterning
MeSH: Angiogenesis*, Ependymoglial Cells*, Retina*, Retinal Vessels*, Animals, Aquaporin 4, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Receptors, Nicotinic, Retinal Ganglion Cells (* major topic)
Topic: Retinal Development and Disorders (Ophthalmology, Medicine), according to OpenAlex
Funding: national institutes of health (R01EY019498, R01EY013528, R21EY037926, P30EY003176); National Science Foundation (DGE 2146752); Howard Hughes Medical Institute (HHMI) (GT17844); University of California Dissertation‐Year Fellowship
Citations: not cited yet (Europe PMC); 52 references in the paper

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 1 match between paragraphs and lines of code.

FellerLabCodeShare/Glia_Vasculature

License: none: the authors keep all their rights
State: the link answers, verified on 31 October 2026
Evidence: files inventoried
Commit: 19c85d9fb208f02e08e75fc488f7eb1bcff76299, 27 May 2026
Languages: MATLAB (4)
Size: 4 files, 4 scripts
Software Heritage: not archived
Found in: “Data Availability Statement”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Statistics and Machine Learning Toolbox (3 files)
Availability: 2 checks, the latest on 31 October 2026: the link answers
  • 31 October 2026: the link answers
  • 1 October 2026: the link answers
4 files
At the source: github.com/FellerLabCodeShare/Glia_Vasculature

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

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Read it in the paper: doi.org/10.1002/glia.70204.

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Version 1, 1 October 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 8 keywords, 12 MeSH terms, 4 funders, 52 references.

Cite

This paper

Monshietehadi, S., Garcia, A. J., Smith, B. E., Tarchick, M., Abhayaratne, K., Conley, A., & Feller, M. B. (2026). Müller Glia-Vasculature Interactions in the Developing Retina. Glia, 74(10), e70204. https://doi.org/10.1002/glia.70204

BibTeX

@article{monshietehadi2026muller,
author = {Monshietehadi, Samira and Garcia, Angel J. and Smith, Benjamin E. and Tarchick, Matthew and Abhayaratne, Kiara and Conley, Aileen and Feller, Marla B.},
title = {{Müller Glia-Vasculature Interactions in the Developing Retina}},
journal = {Glia},
year = {2026},
month = oct,
volume = {74},
number = {10},
pages = {e70204},
publisher = {Wiley},
issn = {0894-1491},
doi = {10.1002/glia.70204},
url = {https://doi.org/10.1002/glia.70204},
pmid = {42552727},
pmcid = {PMC13438127}
}

RIS

TY - JOUR
AU - Monshietehadi, Samira
AU - Garcia, Angel J.
AU - Smith, Benjamin E.
AU - Tarchick, Matthew
AU - Abhayaratne, Kiara
AU - Conley, Aileen
AU - Feller, Marla B.
TI - Müller Glia-Vasculature Interactions in the Developing Retina
T2 - Glia
J2 - Glia
PY - 2026
DA - 2026/10/01
VL - 74
IS - 10
SP - e70204
SN - 0894-1491
PB - Wiley
DO - 10.1002/glia.70204
UR - https://doi.org/10.1002/glia.70204
LA - en
ER -

CSL-JSON

{
"id": "10.1002/glia.70204",
"type": "article-journal",
"title": "Müller Glia-Vasculature Interactions in the Developing Retina",
"container-title": "Glia",
"author": [
{
"family": "Monshietehadi",
"given": "Samira"
},
{
"family": "Garcia",
"given": "Angel J."
},
{
"family": "Smith",
"given": "Benjamin E."
},
{
"family": "Tarchick",
"given": "Matthew"
},
{
"family": "Abhayaratne",
"given": "Kiara"
},
{
"family": "Conley",
"given": "Aileen"
},
{
"family": "Feller",
"given": "Marla B."
}
],
"container-title-short": "Glia",
"volume": "74",
"issue": "10",
"page": "e70204",
"DOI": "10.1002/glia.70204",
"PMID": "42552727",
"PMCID": "PMC13438127",
"ISSN": "0894-1491",
"publisher": "Wiley",
"URL": "https://doi.org/10.1002/glia.70204",
"language": "en",
"issued": {
"date-parts": [
[
2026,
10,
1
]
]
}
}

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