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

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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;
18. %% 【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
19. % Fb_filterData_frameDeletion;
20. % Ha_plotDFF_traces;
21. % Pa_extractGCaMPevents;
22. % Ga_heatMap_raw;
23. % Ia_aveProj_withROI;
24. % La_calculateDistance;
25. % Ma_calculateCorrelation;
26. % Nb_sortedCorrelation_heatMap;
27. % Oa_correlation_ROImap;
28. % Kc_calculateAUC_batch;
30. %% 【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
31. % Ea_filterData_delete; % 切记前往Ea修改需要更改的具体ROI
32. % Ha_plotDFF_traces;
33. % Ga_heatMap_raw;
34. % Pa_extractGCaMPevents;
35. % Ia_aveProj_withROI;
36. % La_calculateDistance;
37. % Ma_calculateCorrelation;
38. % Nb_sortedCorrelation_heatMap;
39. % Oa_correlation_ROImap;
41. 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 Su^4,5, Xiaoqin Lian⁶, Bowen Ren⁷, Chuchu Qi⁸, Jialong Li⁸, Mei Fu¹, Tongtong Gao^1,9, Zhihan Bai^4,5, Minghan Li¹⁰, Dihan Lu¹¹, Na Zhou⁹, Shiqian Shen¹², Wenting Wang⁸, Qian Chen^1,4,5,2,3,6

ORCID iDs: Weiyi Ye, Bowen Ren, Wenting Wang

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

Institutions: Chinese Academy of Sciences (China); Shanghai Institute of Materia Medica (China); Nanjing University of Chinese Medicine (China); Zunyi Medical University (China); University of Chinese Academy of Sciences (China); Guiyang Medical University (China); The Royal Free Hospital (United Kingdom); University College London (United Kingdom); Air Force Medical University (China); Macau University of Science and Technology (Macao SAR China); Fudan University (China); Sun Yat-sen University (China); The First Affiliated Hospital, Sun Yat-sen University (China); Harvard University (United States); Massachusetts General Hospital (United States)

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

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.

Repositories

Its files are read in the Code ↔ Paper reader above.

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

Tools: Statistics and Machine Learning Toolbox (8 files), Signal Processing Toolbox (5 files), Image Processing Toolbox (3 files), Optimization Toolbox (2 files)

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

• AAA_BatchAnalysis.m — MATLAB, 41 lines
• AAA_BatchEvent.m — MATLAB, 69 lines
• Aa_saveData.m — MATLAB, 51 lines
• Ba_copyData.m — MATLAB, 16 lines
• Ca_maskCoordinates.m — MATLAB, 40 lines
• Da_denoised_and_deconvolve.m — MATLAB, 36 lines
• Ea_filterData_delete.m — MATLAB, 30 lines
• Eb_filterData_keep.m — MATLAB, 22 lines
• Ec_filterData_range.m — MATLAB, 33 lines
• Ed_filterData_autoByEvent.m — MATLAB, 35 lines
• Fa_filterData_frameDuration.m — MATLAB, 23 lines
• Fb_filterData_frameDeletion.m — MATLAB, 27 lines
• Ga_heatMap_raw.m — MATLAB, 67 lines
• Gb_heatMap_normalized.m — MATLAB, 65 lines
• Ha_plotDFF_traces.m — MATLAB, 61 lines
• Hb_plotEVent.m — MATLAB, 63 lines
• He_plotDFF_traces_afterEd.m — MATLAB, 61 lines
• Ia_aveProj_withROI.m — MATLAB, 49 lines
• Ib_actMap_aveMap.m — MATLAB, 43 lines
• Ja_rankData_auto.m — MATLAB, 37 lines
• Jb_rankData_manual.m — MATLAB, 24 lines
• Ka_calculateAUC.m — MATLAB, 32 lines
• Kb_calculateAUC_wholeTrace.m — MATLAB, 24 lines
• Kc_calculateAUC_batch.m — MATLAB, 37 lines
• La_calculateDistance.m — MATLAB, 15 lines
• Ma_calculateCorrelation.m — MATLAB, 27 lines
• Na_correlation_heatMap.m — MATLAB, 45 lines
• Nb_sortedCorrelation_heatMap.m — MATLAB, 46 lines
• OASIS_matlab-master/A_denoised_and_deconvolve.m — MATLAB, 28 lines
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• tool/ia_aveProj_withROI.m — MATLAB, 42 lines
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• tool/ka_calculateAUC.m — MATLAB, 32 lines
• tool/kb_calculateAUC_zscore.m — MATLAB, 44 lines
• tool/kc_calculateAUC_whole.m — MATLAB, 32 lines
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• tool/mb_corrlateWithDistance.m — MATLAB, 82 lines
• tool/mc_correlationLineChart.m — MATLAB, 43 lines
• tool/merge_twoPhoton_images.m — MATLAB, 37 lines
• tool/na_correlationMap.m — MATLAB, 51 lines
• tool/nb_sortedCorrelationMap.m — MATLAB, 60 lines
• tool/oa_corrLineWithROI.m — MATLAB, 67 lines
• tool/ob_individualROI.m — MATLAB, 68 lines
• tool/oc_individualROI_subplot.m — MATLAB, 38 lines
• tool/p_analyzedCaTraces.m — MATLAB, 55 lines
• tool/pa_extractGCaMPevents.m — MATLAB, 73 lines
• tool/pa_extractGCaMPevents_MAD_MAD.m — MATLAB, 80 lines
• tool/pa_extractGCaMPevents_Mean_MAD.m — MATLAB, 80 lines
• tool/pb_analyzeEvent.m — MATLAB, 57 lines
• tool/progress.m — MATLAB, 82 lines
• tool/qa_extractFrameIntensity.m — MATLAB, 14 lines
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• tool/qc_smooth_df_image.m — MATLAB, 50 lines
• tool/qd_fileNameCombination.m — MATLAB, 6 lines
• tool/qe_wholeFrameMap.m — MATLAB, 51 lines

At the source: doi.org/10.5281/zenodo.19838893

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

Tools: Statistics and Machine Learning Toolbox (25 files), Image Processing Toolbox (7 files), Curve Fitting Toolbox (5 files), Signal Processing Toolbox (4 files), boundedline (3 files), Optimization Toolbox (2 files)

Availability: 1 check, the latest on 27 September 2026: the link answers

• 27 September 2026: the link answers

1,141 files

• OASIS_matlab/deconvolveCa.m — MATLAB, 355 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/AXfun.m — MATLAB, 55 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Arrow.m — MATLAB, 41 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/HKMcorr.m — MATLAB, 36 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/HKMdirfun.m — MATLAB, 50 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/HKMpred.m — MATLAB, 88 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/HKMrhsfun.m — MATLAB, 99 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexMatvec.c — C, 168 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexProd2.c — C, 305 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexProd2nz.c — C, 193 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexexpand.c — C, 64 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexinprod.c — C, 153 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexmat.c — C, 341 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexnnz.c — C, 68 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexqops.c — C, 143 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexschur.c — C, 471 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexschurfun.c — C, 147 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexskron.c — C, 282 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexsmat.c — C, 454 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mexsvec.c — C, 779 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mextriang.c — C, 174 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Mexfun/mextriangsp.c — C, 129 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/NTcorr.m — MATLAB, 38 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/NTdirfun.m — MATLAB, 48 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/NTpred.m — MATLAB, 65 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/NTrhsfun.m — MATLAB, 118 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/NTscaling.m — MATLAB, 52 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Prod2.m — MATLAB, 59 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/Prod3.m — MATLAB, 53 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/SDPT3data_SEDUMIdata.m — MATLAB, 143 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/SDPT3soln_SEDUMIsoln.m — MATLAB, 113 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/SDPvalBounds.m — MATLAB, 69 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/blkbarrier.m — MATLAB, 44 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/blkcholfun.m — MATLAB, 50 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/blkeig.m — MATLAB, 80 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/blktrace.m — MATLAB, 68 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/checkdense.m — MATLAB, 25 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/checkdepconstr.m — MATLAB, 209 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/combine_blk.m — MATLAB, 83 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/convertRcone.m — MATLAB, 29 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/degeneracy.m — MATLAB, 133 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/linsysolve.m — MATLAB, 230 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/mybicgstab.m — MATLAB, 139 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/mytime.m — MATLAB, 28 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/randmat.m — MATLAB, 30 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/read_sdpa.m — MATLAB, 245 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/read_sedumi.m — MATLAB, 222 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/scaling.m — MATLAB, 78 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/schurmat_lblk.m — MATLAB, 37 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/schurmat_qblk.m — MATLAB, 102 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/schurmat_sblk.m — MATLAB, 130 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/skron.m — MATLAB, 50 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/sqlpmain.m — MATLAB, 818 lines
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• OASIS_matlab/packages/cvx/sdpt3/Solver/sqlpu2lblk.m — MATLAB, 90 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/steplength.m — MATLAB, 181 lines
• OASIS_matlab/packages/cvx/sdpt3/Solver/svec.m — MATLAB, 75 lines
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• OASIS_matlab/packages/cvx/sdpt3/install_sdpt3.m — MATLAB, 195 lines
• OASIS_matlab/packages/cvx/sdpt3/sdpt3.m — MATLAB, 360 lines
• OASIS_matlab/packages/cvx/sedumi/Amul.m — MATLAB, 57 lines
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• OASIS_matlab/packages/cvx/sedumi/adendotd.m — MATLAB, 42 lines
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• OASIS_matlab/packages/cvx/sedumi/asmDxq.m — MATLAB, 69 lines
• OASIS_matlab/packages/cvx/sedumi/auxfwdpr1.c — C, 122 lines
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• OASIS_matlab/packages/cvx/sedumi/blkchol.c — C, 440 lines
• OASIS_matlab/packages/cvx/sedumi/blkchol.m — MATLAB, 60 lines
• OASIS_matlab/packages/cvx/sedumi/blkchol2.c — C, 558 lines
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• OASIS_matlab/packages/cvx/sedumi/blksdp.h — C/C++, 194 lines
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• OASIS_matlab/packages/cvx/sedumi/eyeK.m — MATLAB, 104 lines
• OASIS_matlab/packages/cvx/sedumi/findblks.c — C, 235 lines
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• OASIS_matlab/packages/cvx/sedumi/fwblkslv.c — C, 320 lines
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• OASIS_matlab/packages/cvx/sedumi/spscale.c — C, 770 lines
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• OASIS_matlab/packages/oasis/test_oasis.m — MATLAB, 34 lines
• OASIS_matlab/packages/oasis/thresholded_nnls.m — MATLAB, 220 lines
• OASIS_matlab/packages/oasis/thresholded_oasisAR1.m — MATLAB, 276 lines
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• OASIS_matlab/packages/oasis/update_g.m — MATLAB, 83 lines
• OASIS_matlab/packages/oasis/update_kernel_exp2.m — MATLAB, 131 lines
• OASIS_matlab/packages/oasis/update_lam.m — MATLAB, 78 lines
• OASIS_matlab/packages/oasis/update_tau.m — MATLAB, 144 lines
• OASIS_matlab/packages/oasis_kernel/choose_smin.m — MATLAB, 42 lines
• OASIS_matlab/packages/oasis_kernel/create_kernel.m — MATLAB, 83 lines
• OASIS_matlab/packages/oasis_kernel/deconvCa.m — MATLAB, 358 lines
• OASIS_matlab/packages/oasis_kernel/dsKernel.m — MATLAB, 42 lines
• OASIS_matlab/packages/oasis_kernel/test_oasis.m — MATLAB, 34 lines
• OASIS_matlab/packages/oasis_kernel/update_kernel_exp2.m — MATLAB, 130 lines
• annotater.m — MATLAB, 321 lines
• autoCode2.m — MATLAB, 121 lines
• csHMAnalysis.m — MATLAB, 254 lines
• csPVConvert.m — MATLAB, 328 lines
• curArif.m — MATLAB, 25 lines
• eventInspector.m — MATLAB, 1,808 lines
• eventParser.m — MATLAB, 91 lines
• extractor.m — MATLAB, 1,618 lines
• eyeTrackBasic.m — MATLAB, 21 lines
• functions/basicOps/bindata.m — MATLAB, 32 lines
• functions/basicOps/bindata2.m — MATLAB, 36 lines
• functions/basicOps/bindataN.m — MATLAB, 39 lines
• functions/basicOps/standardError.m — MATLAB, 10 lines
• functions/behavior/binDprime.m — MATLAB, 48 lines
• functions/behavior/filterTrials.m — MATLAB, 450 lines
• functions/behavior/filterTrials2.m — MATLAB, 380 lines
• functions/behavior/filterTrials3.m — MATLAB, 418 lines
• functions/behavior/functions/cadStrap.m — MATLAB, 112 lines
• functions/behavior/functions/crtiloc.m — MATLAB, 4 lines
• functions/behavior/functions/dprime.m — MATLAB, 4 lines
• functions/behavior/functions/nanconv.m — MATLAB, 40 lines
• functions/behavior/getBehavioralStuff.m — MATLAB, 61 lines
• functions/behavior/getSpeeds2.m — MATLAB, 39 lines
• functions/behavior/lickRaster.m — MATLAB, 497 lines
• functions/cadROCf.m — MATLAB, 92 lines
• functions/csVisual/binImages.m — MATLAB, 14 lines
• functions/csVisual/binarizeResponse.m — MATLAB, 11 lines
• functions/csVisual/bootStrapDifferences.m — MATLAB, 69 lines
• functions/csVisual/checkStackBitDepth.m — MATLAB, 12 lines
• functions/csVisual/clipExtract.m — MATLAB, 30 lines
• functions/csVisual/combineStacks.m — MATLAB, 29 lines
• functions/csVisual/csHDFImport.m — MATLAB, 14 lines
• functions/csVisual/csParser.m — MATLAB, 84 lines
• functions/csVisual/csParser2.m — MATLAB, 112 lines
• functions/csVisual/decodeShaftEncoder.m — MATLAB, 39 lines
• functions/csVisual/flattenROIs.m — MATLAB, 10 lines
• functions/csVisual/getStateSamps.m — MATLAB, 32 lines
• functions/csVisual/hmTrigger.m — MATLAB, 52 lines
• functions/csVisual/nPointDPrime.m — MATLAB, 35 lines
• functions/csVisual/plotDeconvolvedCell.m — MATLAB, 21 lines
• functions/csVisual/regFrame.m — MATLAB, 4 lines
• functions/csVisual/rsCaData.m — MATLAB, 26 lines
• functions/csaqua.m — MATLAB, 15 lines
• functions/csblue.m — MATLAB, 15 lines
• functions/csginput.m — MATLAB, 311 lines
• functions/csgreen.m — MATLAB, 15 lines
• functions/cspurple.m — MATLAB, 15 lines
• functions/csred.m — MATLAB, 15 lines
• functions/fDataProcessing/baselineData.m — MATLAB, 32 lines
• functions/fDataProcessing/batchDeltaF.m — MATLAB, 12 lines
• functions/fDataProcessing/batchSmooth.m — MATLAB, 66 lines
• functions/fDataProcessing/blZscore.m — MATLAB, 20 lines
• functions/fDataProcessing/computeQunatileCutoffs.m — MATLAB, 41 lines
• functions/fDataProcessing/reduceStack.m — MATLAB, 37 lines
• functions/fDataProcessing/slidingBaseline.m — MATLAB, 42 lines
• functions/generalMatlab/remap.m — MATLAB, 53 lines
• functions/generalMatlab/unpackStruct.m — MATLAB, 31 lines
• functions/graphTheory/cmccomb-gplot3/gplot3.m — MATLAB, 66 lines
• functions/graphTheory/cmccomb-gplot3/test_gplot3.m — MATLAB, 11 lines
• functions/iagSpecific/checkForWSVar.m — MATLAB, 9 lines
• functions/iagSpecific/deleteROI.m — MATLAB, 69 lines
• functions/iagSpecific/doXInWSOn.m — MATLAB, 3 lines
• functions/iagSpecific/recatROI.m — MATLAB, 69 lines
• functions/imageAnalysis/applyRegTransforms.m — MATLAB, 30 lines
• functions/imageAnalysis/applyTransformsToStack.m — MATLAB, 24 lines
• functions/imageAnalysis/averageEveryN.m — MATLAB, 10 lines
• functions/imageAnalysis/averageEveryNi.m — MATLAB, 10 lines
• functions/imageAnalysis/bandPassData.m — MATLAB, 25 lines
• functions/imageAnalysis/cellDistance.m — MATLAB, 9 lines
• functions/imageAnalysis/centerOfMass.m — MATLAB, 78 lines
• functions/imageAnalysis/dftregistration.m — MATLAB, 234 lines
• functions/imageAnalysis/dftregistrationUd.m — MATLAB, 226 lines
• functions/imageAnalysis/eventDetection.m — MATLAB, 274 lines
• functions/imageAnalysis/getMeansFromMasks.m — MATLAB, 8 lines
• functions/imageAnalysis/inferRunFromRegistration.m — MATLAB, 13 lines
• functions/imageAnalysis/localnormalize.m — MATLAB, 19 lines
• functions/imageAnalysis/overalyRois.m — MATLAB, 13 lines
• functions/imageAnalysis/playMov.m — MATLAB, 34 lines
• functions/imageAnalysis/playMov2.m — MATLAB, 55 lines
• functions/imageAnalysis/playMov3.m — MATLAB, 25 lines
• functions/imageAnalysis/plotImageWRois.m — MATLAB, 20 lines
• functions/imageAnalysis/resortImageFileMap.m — MATLAB, 10 lines
• functions/imageAnalysis/stackMean.m — MATLAB, 18 lines
• functions/infoTheory/MutualInformation.m — MATLAB, 30 lines
• functions/nonnegfac/example_ncp.m — MATLAB, 66 lines
• functions/nonnegfac/example_nmf_1.m — MATLAB, 27 lines
• functions/nonnegfac/example_nmf_2.m — MATLAB, 49 lines
• functions/nonnegfac/ncp.m — MATLAB, 465 lines
• functions/nonnegfac/nmf.m — MATLAB, 680 lines
• functions/nonnegfac/nnls1_asgivens.m — MATLAB, 160 lines
• functions/nonnegfac/nnlsm_activeset.m — MATLAB, 135 lines
• functions/nonnegfac/nnlsm_blockpivot.m — MATLAB, 119 lines
• functions/nonnegfac/normalEqComb.m — MATLAB, 62 lines
• functions/plotCellWithStims.m — MATLAB, 27 lines
• functions/plotting/HIST2.M — MATLAB, 78 lines
• functions/plotting/HISTD.M — MATLAB, 44 lines
• functions/plotting/bplot.m — MATLAB, 401 lines
• functions/plotting/histdiag.m — MATLAB, 50 lines
• functions/plotting/kakearney-boundedline/Inpaint_nans/demo/inpaint_nans_demo_old.m — MATLAB, 42 lines
• functions/plotting/kakearney-boundedline/Inpaint_nans/doc/methods_of_inpaint_nans.m — MATLAB, 187 lines
• functions/plotting/kakearney-boundedline/Inpaint_nans/inpaint_nans.m — MATLAB, 1 line
• functions/plotting/kakearney-boundedline/Inpaint_nans/inpaint_nans_bc.m — MATLAB, 1 line
• functions/plotting/kakearney-boundedline/Inpaint_nans/inpaint_nans_demo.m — MATLAB, 43 lines
• functions/plotting/kakearney-boundedline/Inpaint_nans/test/test_main.m — MATLAB, 178 lines
• functions/plotting/kakearney-boundedline/boundedline/boundedline.m — MATLAB, 457 lines
• functions/plotting/kakearney-boundedline/boundedline/outlinebounds.m — MATLAB, 37 lines
• functions/plotting/kakearney-boundedline/catuneven/catuneven.m — MATLAB, 53 lines
• functions/plotting/kakearney-boundedline/singlepatch/singlepatch.m — MATLAB, 65 lines
• functions/plotting/nhist.m — MATLAB, 2,149 lines
• functions/plotting/overalyRois.m — MATLAB, 13 lines
• functions/plotting/plot2svg/demo_3d_plot2svg.m — MATLAB, 14 lines
• functions/plotting/plot2svg/demo_svg_water.m — MATLAB, 76 lines
• functions/plotting/plot2svg/plot2svg.m — MATLAB, 3,156 lines
• functions/plotting/plot2svg/simulink2svg.m — MATLAB, 17 lines
• functions/plotting/plot2svg/svgBoundingBox.m — MATLAB, 23 lines
• functions/plotting/plot2svg/svgComposite.m — MATLAB, 33 lines
• functions/plotting/plot2svg/svgGaussianBlur.m — MATLAB, 25 lines
• functions/plotting/plot2svg/svgImage.m — MATLAB, 26 lines
• functions/plotting/plot2svg/svgLuminanceToAlpha.m — MATLAB, 24 lines
• functions/plotting/plot2svg/svgOffset.m — MATLAB, 25 lines
• functions/plotting/plot2svg/svgSpecularLightingDistant.m — MATLAB, 34 lines
• functions/plotting/plot2svg/svgTurbulence.m — MATLAB, 30 lines
• functions/plotting/plot2svg/tutorial_filters.m — MATLAB, 133 lines
• functions/plotting/plot2svg/tutorial_plot2svg.m — MATLAB, 260 lines
• functions/plotting/plotImageWRois.m — MATLAB, 20 lines
• functions/plotting/plotNeuro.m — MATLAB, 7 lines
• functions/plotting/plotNeuroHit.m — MATLAB, 7 lines
• functions/plotting/plotNeuroMiss.m — MATLAB, 7 lines
• functions/plotting/plotTrialTrain.m — MATLAB, 13 lines
• functions/plotting/plotTrialTrain2.m — MATLAB, 13 lines
• functions/plotting/plotp.m — MATLAB, 12 lines
• functions/plotting/saveHighPDF.m — MATLAB, 5 lines
• functions/plotting/venn.m — MATLAB, 1,006 lines
• functions/plotting/vennX.m — MATLAB, 344 lines
• functions/save2pdf.m — MATLAB, 67 lines
• functions/stats/HartigansDipSignifTest.m — MATLAB, 29 lines
• functions/stats/HartigansDipTest.m — MATLAB, 303 lines
• functions/stats/bsTest.m — MATLAB, 63 lines
• functions/stats/dpSig.m — MATLAB, 6 lines
• functions/stats/findDrivenCells.m — MATLAB, 29 lines
• functions/stats/jnMeanByTrials.m — MATLAB, 10 lines
• functions/stats/randomFraction.m — MATLAB, 17 lines
• functions/stats/simNorm.m — MATLAB, 8 lines
• functions/timeSeries/Preprocess/abstrans.m — MATLAB, 15 lines
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• functions/timeSeries/Preprocess/center.m — MATLAB, 19 lines
• functions/timeSeries/Preprocess/msc.m — MATLAB, 32 lines
• functions/timeSeries/Preprocess/normaliz.m — MATLAB, 21 lines
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• functions/timeSeries/Preprocess/transabs.m — MATLAB, 15 lines
• functions/timeSeries/abfload.m — MATLAB, 1,451 lines
• functions/timeSeries/bandPassData.m — MATLAB, 25 lines
• functions/timeSeries/baselineData.m — MATLAB, 13 lines
• functions/timeSeries/baselineMat.m — MATLAB, 10 lines
• functions/timeSeries/bf.m — MATLAB, 143 lines
• functions/timeSeries/expsmooth.m — MATLAB, 113 lines
• functions/timeSeries/ezfft.m — MATLAB, 177 lines
• functions/timeSeries/fixgaps.m — MATLAB, 19 lines
• functions/timeSeries/getNoiseCor.m — MATLAB, 27 lines
• functions/timeSeries/getNoiseCorShuf.m — MATLAB, 30 lines
• functions/timeSeries/getNoiseCorSingle.m — MATLAB, 29 lines
• functions/timeSeries/nPointCor.m — MATLAB, 35 lines
• functions/timeSeries/nPointCor2.m — MATLAB, 41 lines
• functions/timeSeries/nPointDeriv.m — MATLAB, 45 lines
• functions/timeSeries/nPointMean.m — MATLAB, 30 lines
• functions/timeSeries/nPointSem.m — MATLAB, 22 lines
• functions/timeSeries/nPointStd.m — MATLAB, 22 lines
• functions/timeSeries/noiseCorr.m — MATLAB, 60 lines
• functions/timeSeries/peakAmps.m — MATLAB, 19 lines
• functions/timeSeries/quickInterp.m — MATLAB, 9 lines
• functions/timeSeries/resamp.m — MATLAB, 31 lines
• functions/timeSeries/resampleCalciumData.m — MATLAB, 26 lines
• functions/timeSeries/shuffleTrialsSimp.m — MATLAB, 10 lines
• functions/timeSeries/simpFFT.m — MATLAB, 3 lines
• functions/timeSeries/stimTrigger.m — MATLAB, 26 lines
• functions/timeSeries/winCountCorr.m — MATLAB, 21 lines
• functions/timeSeries/windowCount.m — MATLAB, 8 lines
• functions/timeSeries/windowCountCorr.m — MATLAB, 21 lines
• functions/timeSeries/zscoreMat.m — MATLAB, 18 lines
• functions/updateVariableNames.m — MATLAB, 12 lines
• functions/xml2struct/xml2struct.m — MATLAB, 183 lines
• importer.m — MATLAB, 1,720 lines
• matBehavior.m — MATLAB, 874 lines
• psth.m — MATLAB, 118 lines
• qianChrisTrigger.m — MATLAB, 187 lines
• qianChrisTrigger2.m — MATLAB, 257 lines
• quickDF.m — MATLAB, 63 lines
• quickSenTime.m — MATLAB, 67 lines
• roiMaker.m — MATLAB, 2,113 lines
• tempScripts/baselineDemo.m — MATLAB, 43 lines
• tempScripts/cleanTrace.m — MATLAB, 105 lines
• tempScripts/dPrimeMov.m — MATLAB, 72 lines
• tempScripts/fullNeuro.m — MATLAB, 36 lines
• tempScripts/killSomaFlags_temp.m — MATLAB, 18 lines
• tempScripts/newExrtract.m — MATLAB, 24 lines
• tempScripts/orient.m — MATLAB, 42 lines
• tempScripts/playROI.m — MATLAB, 65 lines
• tempScripts/quickExt3.m — MATLAB, 34 lines
• tempScripts/quickExt4.m — MATLAB, 30 lines
• tempScripts/tClustPlot.m — MATLAB, 31 lines
• tempScripts/ttrig.m — MATLAB, 67 lines
• LICENSE.txt — License, 21 lines
• README.md — Text, 20 lines

At the source: github.com/cdeister/imageAnalysis_gui

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:

• 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
• 2,163 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.

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
• it says that the code is available on request

Read it in the paper: doi.org/10.1016/j.crmeth.2026.101472.

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 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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"type": "article-journal",
"title": "Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB",
"container-title": "Cell reports methods",
"author": [
{
"family": "Ye",
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},
{
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{
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{
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{
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{
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},
{
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{
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"given": "Chuchu"
},
{
"family": "Li",
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},
{
"family": "Fu",
"given": "Mei"
},
{
"family": "Gao",
"given": "Tongtong"
},
{
"family": "Bai",
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},
{
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},
{
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"given": "Dihan"
},
{
"family": "Zhou",
"given": "Na"
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{
"family": "Shen",
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},
{
"family": "Wang",
"given": "Wenting"
},
{
"family": "Chen",
"given": "Qian"
}
],
"container-title-short": "Cell Rep Methods",
"volume": "6",
"issue": "7",
"page": "101472",
"DOI": "10.1016/j.crmeth.2026.101472",
"PMID": "42225069",
"PMCID": "PMC13390054",
"ISSN": "2667-2375",
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"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
1
]
]
}
}

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