Functional and structural characterization of dendritic spine pathology in a mouse model of tauopathy.

Code ↔ Paper

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[1] § STAR★Methods › Method details › Structural characterization of dendritic spines ↔ util/defaultparameter.m, the whole file · a weak match · score 0.65 · spine turnover module, motion correction, ratio, segmentation, dendritic

Paper

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The authors' code

MATLAB · 64 lines · 4.7 KB · GPL-3.0 · 1 match

function para_default = defaultparameter
% ------------------ edit with caution ---------------------------------
%% movie denoise for feature detection (Don't change these parameters unless you are confident)
para_default.GaussKernel = [4, 4, 2]; % movie denoise kernel (kernel size, kernel size, kernel SD)
para_default.maxLength = 4000; % default dendritic width (pixel)
%% parameter to feature segmentation
para_default.linewidth = 6; % default dendritic width (pixel) (popup variable in GUI)
para_default.th_grad = 2; % feature segmentation at 1/th_grad of the correlation map
% increase this value would generate larger segmentation,
% change range > 1
para_default.w = 3; % feature segmentation neighborhood = w*linewidth
% increase the value, correlation map would be computed from a larger neighborhood
%% parameter to auto feature detection
para_default.minarea = 5; % minimal allowed feature size (pixel)
para_default.maxareagrad = 4; % maximal allowed feature area (pixel) = linewidth*maxareagrad
para_default.MaxAR = 4; % maximal allowed feature aspect ratio
para_default.autofeature = [2, 3.5]; % parameter for autofeature detection (don't change unless you are confident)
para_default.autofeature_bg = 0.3; % background thresholding parameter
% below this fraction of intensity
% pixel will be counted as
% background if not manually
% selecting background
para_default.ifbg = 0; % if manually select background for auto detection
% set to 1, a window would pupup
% allow users to select a background
% area during autofeature detection. Facilitate
% autodetection
para_default.shaftlength = 60; % default shaft length in pixel (popup variable in GUI)
para_default.spinedist = 3; % distance from dendrites for autodetection
% spine search: spinedist * linewidth
%% cross-session alignment (Don't change these parameters unless you are confident)
para_default.ops.withrotation = 1; % alignment with rotation 0(without)/1(with)
para_default.ops.maxIter = 150; % max iteration
para_default.ops.tot = 10^-4; % max tolerance
para_default.ops.distTh = [2, 50]; % [min max] distance threshold
para_default.ops.dispreg = 0; % display
para_default.ops.pointsdetection = [2, 2.5, 2]; % point cloud detection parameters
%% motion correction (Don't change these parameters unless you are confident)
para_default.RegPara.PhaseCorrelation = 1; % set to 0 for non-whitened cross-correlation
para_default.RegPara.SubPixel = Inf; % 2 is alignment by 0.5 pixel, Inf is the exact number from phase correlation
para_default.RegPara.maxDispPerFrame = []; % maximal displacement per frame. recommend [20, 20];
% If empty, values set by 3.5*SD of displacement at initial alignment
% Smaller value is not recommended
para_default.RegPara.lowCorr = 0.1; % minimal registered-to-target correlation. Larger value is not recommended
% initialize motion correction
para_default.RegPara.NiterPrealign = 20; % Number of iteration for initial registrition
para_default.RegPara.iniSearchiter = 5; % Max iteration for chunk searching for initial registrition.
para_default.RegPara.FrameNoiniAlign = 100; % Number of frames for initial alignment.
% This value would be bounded by system memory
% and video length in processing
para_default.RegPara.MinCorr_initial = 0.2; % chunk search continue when initial registrition correlation below this value
%% denoise trace (Input Mapping and Spine Turnover module)
para_default.Denoise.movingaverage = 5; % moving average window size
para_default.Denoise.gaussfilt = [10, 0.3, 20]; % gaussian filtering [fps, signal filter kernel, baseline filter kernel]
para_default.spineRetain = 10; % threshold for mapping cross-session spines

defaultparameter.m at commit c94c78e, under GPL-3.0 · at the source

Overview

Authors: Liam M. Adsit^1,2, Kyle Cekada^2,3, Ikuko T. Smith^1,2,3

ORCID iDs: Ikuko T. Smith

Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA 93106, USA

Institutions: University of California, Santa Barbara (United States)

Journal: iScience, volume 29, issue 9, article 117187

Dates: received 9 February 2026; accepted 28 July 2026; published online 14 August 2026

Type: Research article · Language: English

License: CC BY-NC

Identifiers: DOI 10.1016/j.isci.2026.117187 · PMID 42643223 · PMCID PMC13503137 · OpenAlex W7164362634

Open access: gold, a free copy (OpenAlex)

Preprint: doi:10.64898/2026.06.08.730960

Status: code verified

Categories: histology / microscopy (modality), mouse (organism), Alzheimer's / dementia (population)

Methods: Spectral & time-frequency, Statistics, Machine learning, Preprocessing, fMRI & imaging, Single-unit activity, calcium imaging

Keywords: neurodegenerative disease, tauopathy, dendrite, dendritic spine, spine loss, spine pathology, input mapping

Topic: Neuroscience and Neuropharmacology Research (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex

Funding: Brain Research Foundation (BRFSG-2019-05); Brain and Behavior Research Foundation NARSAD Young Investigator Grant (30481); NIH (R01NS128079)

Citations: not cited yet (Europe PMC); 77 references in the paper

Research resources: Anti-MAP2 RRID:AB_2138153, AT8 RRID:AB_223647, Goat anti-mouse Alexa 594 RRID:AB_2534073, Goat anti-chicken Alexa 488 RRID:AB_2534096, ImageJ RRID:SCR_003070

Abstract

Abnormal deposition of the microtubule-associated protein tau has long been associated with spine loss and neuronal death in neurodegenerative diseases. Elucidating how pathological tau affects synaptic activity in vivo and whether individual synaptic properties dictate the survival fate of dendritic spines is central to understanding disease progression. Here we examined the visual response properties of layer 2/3 primary visual cortical dendrites and spines, using longitudinal two-photon calcium imaging in the P301S mouse model of tauopathy. Neuronal outputs in tau mutant mice were hyperactive and poorly tuned whereas dendritic spine responses were also poorly tuned but hypoactive. Moreover, in controls, stable spines were larger in size and more sharply tuned but less active compared to those that turned over. Such a function-to-structure relationship was absent in mutants. Our findings illustrate how tauopathy disrupts the preferential maintenance of well-tuned inputs in healthy neural circuitry, resulting in poorly tuned visual responses.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

gtzook/iSLAB-data-analysis

License: none: the authors keep all their rights

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: 86660790d6715318eb2fdc011771dba402e33949, 7 April 2026

Languages: MATLAB (30)

Size: 64 files, 30 scripts

Software Heritage: not archived

Found in: “Data and code availability”

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Optimization Toolbox (1 file), Signal Processing Toolbox (1 file)

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

27 September 2026: the link answers

30 files

Extraction Functions/data_processing/detectSpikes.m, MATLAB, 26 lines
Extraction Functions/data_processing/detectSpikes_helper.m, MATLAB, 41 lines
Extraction Functions/data_processing/get_snips_and_stats.m, MATLAB, 113 lines
Extraction Functions/data_processing/get_snips_and_stats_helper.m, MATLAB, 97 lines
Extraction Functions/data_processing/processROI.m, MATLAB, 18 lines
Extraction Functions/data_processing/process_spikes.m, MATLAB, 28 lines
Extraction Functions/data_processing/remove_tug_dff.m, MATLAB, 30 lines
Extraction Functions/data_processing/subtract_dendrite.m, MATLAB, 21 lines
Extraction Functions/misc_helpers/make_stats_mat.m, MATLAB, 7 lines
Extraction Functions/misc_helpers/mean_std_sem.m, MATLAB, 7 lines
Extraction Functions/misc_helpers/mean_std_sem_list.m, MATLAB, 7 lines
Extraction Functions/misc_helpers/med_and_mad.m, MATLAB, 7 lines
Extraction Functions/misc_helpers/movquant.m, MATLAB, 12 lines
Extraction Functions/misc_helpers/plot_exp.m, MATLAB, 16 lines
Extraction Functions/misc_helpers/preprocessFile.m, MATLAB, 19 lines
Extraction Functions/misc_helpers/selectFiles.m, MATLAB, 14 lines
Extraction Functions/misc_helpers/sl_ema.m, MATLAB, 18 lines
Extraction Functions/tuning/compute_osi.m, MATLAB, 29 lines
Extraction Functions/tuning/compute_snr.m, MATLAB, 10 lines
Extraction Functions/tuning/compute_tuning.m, MATLAB, 63 lines
Postprocessing Functions/detect_hotspots.m, MATLAB, 96 lines
Postprocessing Functions/gaussian_fit.m, MATLAB, 54 lines
Postprocessing Functions/plot_bimodal_gaussian.m, MATLAB, 29 lines
Postprocessing Functions/plot_unimodal_gaussian.m, MATLAB, 25 lines
Postprocessing Functions/tuning_plot.m, MATLAB, 9 lines
alt/data_extraction2.m, MATLAB, 77 lines
alt/processROI2.m, MATLAB, 18 lines
alt/remove_tug_dff2.m, MATLAB, 49 lines
data_extraction.m, MATLAB, 71 lines
postprocessing.m, MATLAB, 509 lines

At the source: github.com/gtzook/iSLAB-data-analysis

yuyiyi/AUTOTUNE_GUIdevelopment

License: GPL-3.0

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: c94c78e31e1f605baa104ccd164953029ccabf15, 6 June 2024

Languages: MATLAB (134)

Size: 150 files, 134 scripts

Software Heritage: not archived

Found in: the text, “Structural characterization of dendritic spines”

Holds: README, license file

Not found: CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Image Processing Toolbox (16 files), Statistics and Machine Learning Toolbox (13 files), Curve Fitting Toolbox (6 files), Parallel Computing Toolbox (5 files), shadedErrorBar (2 files)

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

27 September 2026: the link answers

136 files

AUTOTUNE.m, MATLAB, 109 lines
featurefun/AutoFeature_detection.m, MATLAB, 57 lines
featurefun/Auto_points.m, MATLAB, 78 lines
featurefun/BatchCallFeatureDetection.m, MATLAB, 102 lines
featurefun/Call_autofeature.m, MATLAB, 27 lines
featurefun/Call_loadbin.m, MATLAB, 47 lines
featurefun/Call_loadmovie.m, MATLAB, 70 lines
featurefun/SegmentationBatch_autoThresh.m, MATLAB, 159 lines
featurefun/Segmentation_autoThresh.m, MATLAB, 128 lines
featurefun/SpineTrace_IndividualMovie.m, MATLAB, 402 lines
featurefun/SpineTrace_batch.m, MATLAB, 236 lines
featurefun/addDendrites.m, MATLAB, 57 lines
featurefun/call_autoshaftDendr.m, MATLAB, 128 lines
featurefun/call_deletefeature.m, MATLAB, 50 lines
featurefun/call_manualspine.m, MATLAB, 64 lines
featurefun/featuredetect_batch_init.m, MATLAB, 80 lines
featurefun/featuredetect_init.m, MATLAB, 48 lines
featurefun/generateDendritemask.m, MATLAB, 8 lines
featurefun/get_spineROImask.m, MATLAB, 18 lines
featurefun/lineSegment.m, MATLAB, 60 lines
featurefun/line_expand.m, MATLAB, 30 lines
featurefun/loadbin_init.m, MATLAB, 59 lines
featurefun/loadmovie_init.m, MATLAB, 51 lines
featurefun/manual_dendrtictrace_v2.m, MATLAB, 146 lines
featurefun/nearestDendrite.m, MATLAB, 179 lines
featurefun/refresh_delete.m, MATLAB, 30 lines
featurefun/refreshspine.m, MATLAB, 26 lines
featurefun/shaftloc.m, MATLAB, 26 lines
featurefun/showbatchfeature.m, MATLAB, 54 lines
generalfun/MovGaussFilter.m, MATLAB, 31 lines
generalfun/MovGaussFilter_v2.m, MATLAB, 27 lines
generalfun/Save_SingleData.m, MATLAB, 207 lines
generalfun/Save_SingleData_bin.m, MATLAB, 180 lines
generalfun/displayGUIplots.m, MATLAB, 122 lines
generalfun/drawploy_custom.m, MATLAB, 15 lines
generalfun/gather_try.m, MATLAB, 6 lines
generalfun/getOr.m, MATLAB, 26 lines
generalfun/getdff.m, MATLAB, 21 lines
generalfun/imwrite2tif.m, MATLAB, 145 lines
generalfun/listselectedfiles.m, MATLAB, 82 lines
generalfun/loadROImaskfile.m, MATLAB, 62 lines
generalfun/saveSpine.m, MATLAB, 21 lines
generalfun/selectsinglefiles.m, MATLAB, 36 lines
generalfun/showROI.m, MATLAB, 11 lines
generalfun/showROI_3D.m, MATLAB, 21 lines
generalfun/showscalebar.m, MATLAB, 7 lines
plotfun/BAPremove_auto.m, MATLAB, 42 lines
plotfun/BAPupdate_CMD.m, MATLAB, 52 lines
plotfun/BAPupdate_GUI.m, MATLAB, 66 lines
plotfun/BehResp_Ana.m, MATLAB, 110 lines
plotfun/DendriticSpine_hist.m, MATLAB, 48 lines
plotfun/F_Preprocess_v2.m, MATLAB, 49 lines
plotfun/FitstampResp.m, MATLAB, 167 lines
plotfun/FitstampResp_customfun.m, MATLAB, 104 lines
plotfun/FitstampResp_v2.m, MATLAB, 197 lines
plotfun/InputMapping.m, MATLAB, 319 lines
plotfun/SelVar.m, MATLAB, 52 lines
plotfun/SelectfeatureForVisual.m, MATLAB, 77 lines
plotfun/Selfeature.m, MATLAB, 48 lines
plotfun/SpineTurnover.m, MATLAB, 163 lines
plotfun/barwitherr.m, MATLAB, 157 lines
plotfun/callBAPsubtract_filt.m, MATLAB, 80 lines
plotfun/callBAPsubtract_master.m, MATLAB, 81 lines
plotfun/call_autoBAP.m, MATLAB, 60 lines
plotfun/call_autoBAP_filt.m, MATLAB, 60 lines
plotfun/call_behresp.m, MATLAB, 129 lines
plotfun/call_gaussfilt.m, MATLAB, 119 lines
plotfun/call_plotsometrace.m, MATLAB, 45 lines
plotfun/call_stampresp.m, MATLAB, 119 lines
plotfun/call_stampresp_v2.m, MATLAB, 134 lines
plotfun/callgaussfilt_master.m, MATLAB, 54 lines
plotfun/calllochist.m, MATLAB, 96 lines
plotfun/callsmoothfilt_master.m, MATLAB, 60 lines
plotfun/circularfit.m, MATLAB, 7 lines
plotfun/featuresel.m, MATLAB, 39 lines
plotfun/input_refresh.m, MATLAB, 37 lines
plotfun/inputmap_init.m, MATLAB, 77 lines
plotfun/inputmap_refreshplot.m, MATLAB, 91 lines
plotfun/loadDataforPlots.m, MATLAB, 285 lines
plotfun/loadcustomfeature.m, MATLAB, 31 lines
plotfun/loadfilesub.m, MATLAB, 39 lines
plotfun/loadframestamp.m, MATLAB, 53 lines
plotfun/loadtrace.m, MATLAB, 232 lines
plotfun/multiplot.m, MATLAB, 63 lines
plotfun/multiplot_multitrace.m, MATLAB, 39 lines
plotfun/multiplot_segment.m, MATLAB, 46 lines
plotfun/plotrawtrace.m, MATLAB, 86 lines
plotfun/pooltrace.m, MATLAB, 94 lines
plotfun/pooltrace_forGaussfilt.m, MATLAB, 38 lines
plotfun/prepBehResp.m, MATLAB, 210 lines
plotfun/prepCrossSessReg.m, MATLAB, 53 lines
plotfun/prepFitting.m, MATLAB, 177 lines
plotfun/prepPlottrace.m, MATLAB, 49 lines
plotfun/prepStampRespPlot.m, MATLAB, 30 lines
plotfun/prep_TurnOverAna.m, MATLAB, 73 lines
plotfun/prep_filt.m, MATLAB, 87 lines
plotfun/shadedErrorBar.m, MATLAB, 162 lines
plotfun/showframestamptbl.m, MATLAB, 24 lines
plotfun/spineEvolveAna.m, MATLAB, 385 lines
plotfun/stampResp.m, MATLAB, 83 lines
plotfun/stampResp_v2.m, MATLAB, 116 lines
plotfun/traceplot22.m, MATLAB, 55 lines
plotfun/wrapped_1gaussian.m, MATLAB, 7 lines
plotfun/wrapped_2gaussian.m, MATLAB, 13 lines
regfun/Call_initialReg.m, MATLAB, 75 lines
regfun/ICP_point_reg.m, MATLAB, 166 lines
regfun/ICP_point_regRTbalance.m, MATLAB, 101 lines
regfun/ICP_point_regRenhance.m, MATLAB, 163 lines
regfun/PointCloud_reg.m, MATLAB, 18 lines
regfun/RegistrationWin.m, MATLAB, 261 lines
regfun/align_iterative_modified.m, MATLAB, 34 lines
regfun/callregistration.m, MATLAB, 33 lines
regfun/cloest_obj.m, MATLAB, 5 lines
regfun/dendrite_regmater.m, MATLAB, 80 lines
regfun/get_imageinfo.m, MATLAB, 90 lines
regfun/icp2.m, MATLAB, 118 lines
regfun/icp_init_translation.m, MATLAB, 18 lines
regfun/phase_reg.m, MATLAB, 163 lines
regfun/pick_reg_init.m, MATLAB, 21 lines
regfun/pointfeature_detect2.m, MATLAB, 71 lines
regfun/reg_NoCrossStack.m, MATLAB, 198 lines
regfun/reg_WithCrossStack.m, MATLAB, 206 lines
regfun/reg_dregmode.m, MATLAB, 43 lines
regfun/reg_iterative.m, MATLAB, 35 lines
regfun/register_movie.m, MATLAB, 38 lines
regfun/registration_init.m, MATLAB, 39 lines
regfun/registration_offsets_modified.m, MATLAB, 151 lines
regfun/saveDregdata.m, MATLAB, 22 lines
regfun/savesubtif.m, MATLAB, 19 lines
regfun/setupCross_SessionReg.m, MATLAB, 158 lines
regfun/showregresult.m, MATLAB, 18 lines
regfun/spineROI_regmater.m, MATLAB, 60 lines
regfun/translate_ROImask.m, MATLAB, 40 lines
util/defaultparameter.m, MATLAB, 64 lines, 1 match
LICENSE, License, 674 lines
README.md, Text, 39 lines

At the source: github.com/yuyiyi/AUTOTUNE_GUIdevelopment.git

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.

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2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
164 scripts, each with its path and the digest of its content;
1 match between paragraphs of the paper and lines of the code (method lexical-v1);
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Data

Datasets cited

data.mendeley.com/datasets/5fxnnjn8vk, at Mendeley Data; found in the text, “Key resources table”

Data and code availability

• All data reported in this paper will be shared by the lead contact upon request. Processed data of calcium imaging have been deposited at Mendeley Data and are publicly available as of the date of publication. The DOI is listed in the key resources table. • All original code has been deposited at GitHub and is publicly available at https://github.com/gtzook/iSLAB-data-analysis as of the date of publication. • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 7 keywords, 3 funders, 75 references, 5 RRIDs.

Cite

This paper

Adsit, L. M., Cekada, K., & Smith, I. T. (2026). Functional and structural characterization of dendritic spine pathology in a mouse model of tauopathy. iScience, 29(9), 117187. https://doi.org/10.1016/j.isci.2026.117187

BibTeX

@article{adsit2026functional, author = {Adsit, Liam M. and Cekada, Kyle and Smith, Ikuko T.}, title = {{Functional and structural characterization of dendritic spine pathology in a mouse model of tauopathy}}, journal = {iScience}, year = {2026}, month = aug, volume = {29}, number = {9}, pages = {117187}, publisher = {Elsevier}, issn = {2589-0042}, doi = {10.1016/j.isci.2026.117187}, url = {https://doi.org/10.1016/j.isci.2026.117187}, pmid = {42643223}, pmcid = {PMC13503137} }

RIS

TY - JOUR AU - Adsit, Liam M. AU - Cekada, Kyle AU - Smith, Ikuko T. TI - Functional and structural characterization of dendritic spine pathology in a mouse model of tauopathy T2 - iScience J2 - iScience PY - 2026 DA - 2026/08/14 VL - 29 IS - 9 SP - 117187 SN - 2589-0042 PB - Elsevier DO - 10.1016/j.isci.2026.117187 UR - https://doi.org/10.1016/j.isci.2026.117187 LA - en ER -

CSL-JSON

{ "id": "10.1016/j.isci.2026.117187", "type": "article-journal", "title": "Functional and structural characterization of dendritic spine pathology in a mouse model of tauopathy", "container-title": "iScience", "author": [ { "family": "Adsit", "given": "Liam M." }, { "family": "Cekada", "given": "Kyle" }, { "family": "Smith", "given": "Ikuko T." } ], "container-title-short": "iScience", "volume": "29", "issue": "9", "page": "117187", "DOI": "10.1016/j.isci.2026.117187", "PMID": "42643223", "PMCID": "PMC13503137", "ISSN": "2589-0042", "publisher": "Elsevier", "URL": "https://doi.org/10.1016/j.isci.2026.117187", "language": "en", "issued": { "date-parts": [ [ 2026, 8, 14 ] ] } }

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