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Microbubble Track-Based Functional Ultrasound Localization Microscopy in Awake Mice.

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Paper

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The authors' code

MATLAB · 56 lines · 2 KB · no license

  1. function [C_track, C_pixel] = run_example()
  2. %RUN_EXAMPLE Reproduce track-based and pixel-based fULM correlation maps.
  4. repositoryRoot = fileparts(mfilename('fullpath'));
  5. addpath(fullfile(repositoryRoot, 'src'));
  7. exampleData = load(fullfile(repositoryRoot, 'data', ...
  8. 'simulation_example.mat'), 'I', 'r', 'trackMaps');
  10. [C_track, ~, trackCountMap] = track_based_correlation( ...
  11. exampleData.I, exampleData.r, exampleData.trackMaps);
  12. C_pixel = pixel_based_correlation(exampleData.I, exampleData.r);
  14. figureHandle = figure('Color', 'w', ...
  15. 'Name', 'TrackBased-fULM example', 'Position', [100 100 1100 480]);
  16. layout = tiledlayout(figureHandle, 1, 2, ...
  17. 'Padding', 'compact', 'TileSpacing', 'compact');
  19. pixelAxes = nexttile(layout);
  20. imagesc(pixelAxes, C_pixel, [-0.4 0.4]);
  21. axis(pixelAxes, 'image');
  22. axis(pixelAxes, 'off');
  23. title(pixelAxes, 'Pixel-based correlation');
  24. colorbar(pixelAxes);
  26. trackAxes = nexttile(layout);
  27. imagesc(trackAxes, C_track, [-0.4 0.4]);
  28. axis(trackAxes, 'image');
  29. axis(trackAxes, 'off');
  30. title(trackAxes, 'Track-based correlation');
  31. colorbar(trackAxes);
  33. colormap(figureHandle, correlation_colormap(256));
  34. title(layout, 'Microbubble track-based fULM simulation example');
  36. fprintf('Loaded %d frames and %d tracks.\n', ...
  37. size(exampleData.I, 3), numel(exampleData.trackMaps));
  38. fprintf('%d pixels were visited by at least one track.\n', ...
  39. nnz(trackCountMap));
  40. end
  42. function colorMap = correlation_colormap(numberColors)
  43. controlPositions = [0 0.2 0.3 0.5 0.53 0.63 1.0];
  44. controlColors = [ ...
  45. 1.0 1.0 0.5; ...
  46. 1.0 0.0 0.0; ...
  47. 0.4 0.2 0.1; ...
  48. 0.0 0.0 0.0; ...
  49. 0.0 0.1 0.1; ...
  50. 0.0 0.1 1.0; ...
  51. 0.6 0.7 0.9];
  52. colorMap = interp1(controlPositions, controlColors, ...
  53. linspace(0, 1, numberColors), 'linear');
  54. colorMap = min(max(colorMap, 0), 1);
  55. colorMap = flipud(colorMap); % Negative: purple; positive: yellow.
  56. end

run_example.m at commit ed7a2a7, no license · at the source

Overview

Authors: Yike Wang1, Matthew R Lowerison2, Zhe Huang2, YiRang Shin2, Bing-Ze Lin3, Pengfei Song3
ORCID iDs: Yike Wang, Matthew R Lowerison, Zhe Huang, YiRang Shin, Bing-Ze Lin, Pengfei Song
  1. Department of Biomedical Engineering, Duke University, Durham, NC 27708 USA, and also with the Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61820 USA
  2. Department of Biomedical Engineering, Duke University, Durham, NC 27708 USA
  3. Department of Biomedical Engineering, Duke University, Durham, NC 27708 USA, and also with the Department of Electrical and Computer Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61820 USA
Institutions: University of Illinois Urbana-Champaign (United States); Duke University (United States)
Journal: IEEE transactions on medical imaging, volume 45, issue 8, pages 4518-4531
Dates: published online August 2026; in print August 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1109/tmi.2026.3704144 · PMID 42308082 · PMCID PMC13491282 · OpenAlex W4413472260
Open access: hybrid, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.08.18.670859
Status: code verified
Categories: other (modality), histology / microscopy (modality), mouse (organism)
Methods: Statistics, Machine learning, Preprocessing, Connectivity, fMRI & imaging
Keywords: Functional ultrasound imaging, ultrasound localization microscopy, awake animal neuroimaging, cerebral blood flow
MeSH: Image Processing, Computer-Assisted*, Microbubbles*, Microscopy*, Animals, Brain, Contrast Media, Mice, Mice, Inbred C57BL, Ultrasonography, Wakefulness (* major topic)
Topic: Photoacoustic and Ultrasonic Imaging (Biomedical Engineering, Engineering), according to OpenAlex
Funding: National Institute of Biomedical Imaging and Bioengineering and the National Institute of Neurological Disorders and Stroke of the National Institutes of Health (R21EB030072); Chan Zuckerberg Initiative (CZI) Ben Berres Early Career Acceleration Award; National Science Foundation CAREER (2237166); NIBIB NIH HHS (R21 EB030072); NINDS NIH HHS (R56 NS131516)
Citations: not cited yet (Europe PMC); 39 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.

ekerwang/TrackBased-fULM

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: ed7a2a77661c152f7ebb1685023dea33c79789b3, 8 August 2026
Languages: MATLAB (5)
Size: 11 files, 5 scripts
Software Heritage: not archived
Found in: the text, “Principles of MB Track-Based fULM”
Holds: README, CITATION.cff, tests
Not found: license file, environment file, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
6 files
At the source: github.com/ekerwang/TrackBased-fULM

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;
  • 5 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • 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.

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 3, 28 September 2026

  • Publisher: n/a → Institute of Electrical and Electronics Engineers

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 4 keywords, 10 MeSH terms, 5 funders, 39 references.

Cite

This paper

Wang, Y., Lowerison, M. R., Huang, Z., Shin, Y., Lin, B.-Z., & Song, P. (2026). Microbubble Track-Based Functional Ultrasound Localization Microscopy in Awake Mice. IEEE transactions on medical imaging, 45(8), 4518-4531. https://doi.org/10.1109/tmi.2026.3704144

BibTeX

@article{wang2026microbubble,
author = {Wang, Yike and Lowerison, Matthew R and Huang, Zhe and Shin, YiRang and Lin, Bing-Ze and Song, Pengfei},
title = {{Microbubble Track-Based Functional Ultrasound Localization Microscopy in Awake Mice}},
journal = {IEEE transactions on medical imaging},
year = {2026},
month = aug,
volume = {45},
number = {8},
pages = {4518--4531},
publisher = {Institute of Electrical and Electronics Engineers},
issn = {0278-0062},
doi = {10.1109/tmi.2026.3704144},
url = {https://doi.org/10.1109/tmi.2026.3704144},
pmid = {42308082},
pmcid = {PMC13491282}
}

RIS

TY - JOUR
AU - Wang, Yike
AU - Lowerison, Matthew R
AU - Huang, Zhe
AU - Shin, YiRang
AU - Lin, Bing-Ze
AU - Song, Pengfei
TI - Microbubble Track-Based Functional Ultrasound Localization Microscopy in Awake Mice
T2 - IEEE transactions on medical imaging
J2 - IEEE Trans Med Imaging
PY - 2026
DA - 2026/08/01
VL - 45
IS - 8
SP - 4518
EP - 4531
SN - 0278-0062
PB - Institute of Electrical and Electronics Engineers
DO - 10.1109/tmi.2026.3704144
UR - https://doi.org/10.1109/tmi.2026.3704144
LA - en
ER -

CSL-JSON

{
"id": "10.1109/tmi.2026.3704144",
"type": "article-journal",
"title": "Microbubble Track-Based Functional Ultrasound Localization Microscopy in Awake Mice",
"container-title": "IEEE transactions on medical imaging",
"author": [
{
"family": "Wang",
"given": "Yike"
},
{
"family": "Lowerison",
"given": "Matthew R"
},
{
"family": "Huang",
"given": "Zhe"
},
{
"family": "Shin",
"given": "YiRang"
},
{
"family": "Lin",
"given": "Bing-Ze"
},
{
"family": "Song",
"given": "Pengfei"
}
],
"container-title-short": "IEEE Trans Med Imaging",
"volume": "45",
"issue": "8",
"page": "4518-4531",
"DOI": "10.1109/tmi.2026.3704144",
"PMID": "42308082",
"PMCID": "PMC13491282",
"ISSN": "0278-0062",
"publisher": "Institute of Electrical and Electronics Engineers",
"URL": "https://doi.org/10.1109/tmi.2026.3704144",
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
1
]
]
}
}

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

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