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Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB.

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Paper

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The authors' code

MATLAB · 41 lines · 1.2 KB · CC-BY-4.0

  1. %% 【方案1】全流程基于event自动化处理
  2. % Ba_copyData;
  3. % Ca_maskCoordinates;
  4. % Da_denoised_and_deconvolve;
  5. % Ha_plotDFF_traces;
  6. % Pa_extractGCaMPevents;
  7. % Ed_filterData_autoByEvent;
  8. % Ha_plotDFF_traces;
  9. % Ga_heatMap_raw;
  10. % Pa_extractGCaMPevents;
  11. % Ia_aveProj_withROI;
  12. % La_calculateDistance;
  13. % Ma_calculateCorrelation;
  14. % Nb_sortedCorrelation_heatMap;
  15. % Oa_correlation_ROImap;
  16. % Kc_calculateAUC_batch;
  17. %% 【方案2】完成方案1运行后,需要使用Fb删除z轴波动的信号。填写完Fb后运行下述程序
  18. % Fb_filterData_frameDeletion;
  19. % Ha_plotDFF_traces;
  20. % Pa_extractGCaMPevents;
  21. % Ga_heatMap_raw;
  22. % Ia_aveProj_withROI;
  23. % La_calculateDistance;
  24. % Ma_calculateCorrelation;
  25. % Nb_sortedCorrelation_heatMap;
  26. % Oa_correlation_ROImap;
  27. % Kc_calculateAUC_batch;
  28. %% 【方案3】如果需要运行Ea删除特定的ROI,填写完Ea后,运行下述程序
  29. % Ea_filterData_delete; % 切记前往Ea修改需要更改的具体ROI
  30. % Ha_plotDFF_traces;
  31. % Ga_heatMap_raw;
  32. % Pa_extractGCaMPevents;
  33. % Ia_aveProj_withROI;
  34. % La_calculateDistance;
  35. % Ma_calculateCorrelation;
  36. % Nb_sortedCorrelation_heatMap;
  37. % Oa_correlation_ROImap;
  38. clear index_delete;

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

Overview

Authors: Weiyi Ye1, Mao Deng1, Sijing Zhao2, Xiaodong Chen3, Simin Su4,5, Xiaoqin Lian6, Bowen Ren7, Chuchu Qi8, Jialong Li8, Mei Fu1, Tongtong Gao1,9, Zhihan Bai4,5, Minghan Li10, Dihan Lu11, Na Zhou9, Shiqian Shen12, Wenting Wang8, Qian Chen1,4,5,2,3,6
  1. Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528403, China
  2. School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210032, China
  3. Zunyi Medical University, Zunyi 563000, China
  4. Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
  5. University of Chinese Academy of Sciences, Beijing 101408, China
  6. Guizhou Medical University, Guiyang 561113, China
  7. Division of Medicine, University College London, Royal Free Campus, London WC1E 6BT, UK
  8. Department of Neurobiology, School of Basic Medicine, Fourth Military Medical University, Xi’an 710032, China
  9. Faculty of Medicine, Macau University of Science and Technology, Macao 999078, China
  10. Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
  11. Department of Anesthesiology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
  12. Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston MA 02171, USA
Journal: Cell reports methods, volume 6, issue 7, article 101472
Dates: received 6 October 2025; accepted 4 May 2026; published online 1 June 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.crmeth.2026.101472 · PMID 42225069 · PMCID PMC13390054 · OpenAlex W7163040972
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: histology / microscopy (modality), optical imaging (calcium, voltage, 2-photon) (modality), mouse (organism)
Methods: Spectral & time-frequency, Statistics, Preprocessing, Evoked potentials, Connectivity, fMRI & imaging, Single-unit activity, calcium imaging
Keywords: developing brain, AAV-PHP.eB, single-neuron labeling, calcium imaging, GCaMP
MeSH: Brain*, Dependovirus*, Neurons*, Staining and Labeling*, Animals, Calcium, Genetic Vectors, Mice, Transduction, Genetic (* major topic)
Topic: Virus-based gene therapy research (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Natural Science Foundation of China (82571764, 82271578, 82271577); Shaanxi Province Health Commission (2023-ZDLSF-47); Key Industry Innovation Chain of Shaanxi; Zhongshan Science and Technology Bureau (CXTD2022013)
Citations: not cited yet (Europe PMC); 42 references in the paper
Research resources: RRID:AB_10711040, RRID:AB_11157799, Goat anti-Chicken Alexa FluorTM488 RRID:AB_142924, Donkey anti-Rabbit Alexa FluorTM555 RRID:AB_162543, Mouse monoclonal anti-GAD67 Antibody RRID:AB_2278725, Donkey anti-Rabbit Alexa FluorTM488 RRID:AB_2535792, Donkey anti-Mouse AlexaFluorTM555 RRID:AB_2536180, Chicken polyclonal Anti-GFP Antibody RRID:AB_300798, Rabbit monoclonal Anti-GFP antibody RRID:AB_305564, MATLAB R2021a RRID:SCR_001622, GraphPad Prism RRID:SCR_002798, ImageJ RRID:SCR_003070, Imaris Filament Tracer RRID:SCR_007366

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.

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Zenodo 19838893

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data and code availability”
Not found: README, 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)
1,024 files

cdeister/imageAnalysis_gui

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 3be6827b5a02c7667d53e6655f01511a0c61f92b, 29 April 2024
Languages: MATLAB (1055), C (71), JavaScript (9), C/C++ (4)
Size: 1,715 files, 1,139 scripts
Software Heritage: not checked
Found in: the text, “Two-photon imaging data analysis”
Holds: README, license file, tests, documentation
Not found: CITATION.cff, environment file, continuous integration
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
1,141 files

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

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Data

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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:

  • it points to the authors' code: Zenodo 19838893
  • it says that the data are available on request
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Read it in the paper: doi.org/10.1016/j.crmeth.2026.101472.

Versions

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Version 2, 28 September 2026

  • Authors: added Wenting Wang (0000-0002-8344-0102); removed Wenting Wang

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 18 authors, 5 keywords, 9 MeSH terms, 4 funders, 42 references, 13 RRIDs.

Cite

This paper

Ye, W., Deng, M., Zhao, S., Chen, X., Su, S., Lian, X., Ren, B., Qi, C., Li, J., Fu, M., Gao, T., Bai, Z., Li, M., Lu, D., Zhou, N., Shen, S., Wang, W., & Chen, Q. (2026). Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB. Cell reports methods, 6(7), 101472. https://doi.org/10.1016/j.crmeth.2026.101472

BibTeX

@article{ye2026rapid,
author = {Ye, Weiyi and Deng, Mao and Zhao, Sijing and Chen, Xiaodong and Su, Simin and Lian, Xiaoqin and Ren, Bowen and Qi, Chuchu and Li, Jialong and Fu, Mei and Gao, Tongtong and Bai, Zhihan and Li, Minghan and Lu, Dihan and Zhou, Na and Shen, Shiqian and Wang, Wenting and Chen, Qian},
title = {{Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB}},
journal = {Cell reports methods},
year = {2026},
month = jun,
volume = {6},
number = {7},
pages = {101472},
publisher = {Elsevier},
issn = {2667-2375},
doi = {10.1016/j.crmeth.2026.101472},
url = {https://doi.org/10.1016/j.crmeth.2026.101472},
pmid = {42225069},
pmcid = {PMC13390054}
}

RIS

TY - JOUR
AU - Ye, Weiyi
AU - Deng, Mao
AU - Zhao, Sijing
AU - Chen, Xiaodong
AU - Su, Simin
AU - Lian, Xiaoqin
AU - Ren, Bowen
AU - Qi, Chuchu
AU - Li, Jialong
AU - Fu, Mei
AU - Gao, Tongtong
AU - Bai, Zhihan
AU - Li, Minghan
AU - Lu, Dihan
AU - Zhou, Na
AU - Shen, Shiqian
AU - Wang, Wenting
AU - Chen, Qian
TI - Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB
T2 - Cell reports methods
J2 - Cell Rep Methods
PY - 2026
DA - 2026/06/01
VL - 6
IS - 7
SP - 101472
SN - 2667-2375
PB - Elsevier
DO - 10.1016/j.crmeth.2026.101472
UR - https://doi.org/10.1016/j.crmeth.2026.101472
LA - en
ER -

CSL-JSON

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"container-title": "Cell reports methods",
"author": [
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