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Male and female mice scent mark during social communication regardless of sexual motivation or partner identity.

Code ↔ Paper

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The 3 matches · 2 of them tie a paragraph to a whole file without given lines: weak matches, whose lines are not tinted
  1. [1] § STAR★METHODS › METHOD DETAILS › Odor-motivated unidirectional scent marking assay ↔ smufMakeEum.m, the whole file · a weak match · score 0.82 · bottom cut, urine detection, green channels, overlay, cameras, tracking · Report a mismatch
  2. [2] § STAR★METHODS › METHOD DETAILS › Odor-motivated unidirectional scent marking assay ↔ smufVideoToPixels.m, lines 30 to 82 · score 0.80 · bottom cut, urine detection, green channels, overlay, video, tracking · Report a mismatch
  3. [3] § STAR★METHODS › METHOD DETAILS › Conspecific-motivated bidirectional scent marking assay ↔ smufMakeEum.m, the whole file · a weak match · score 0.65 · green channel, urine spot, cropped, camera, cage, thresholding · Report a mismatch

Paper

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The authors' code

MATLAB · 112 lines · 5 KB · GPL-3.0 · 2 matches

  1. function [eum] = smufMakeEum( filepath, mouseNum, cageMask )
  2. %% smufMakeEum: function to read in SMUF video frame and create End Urine Map (EUM)
  3. %
  4. % This function allows selection of ROIs to exclude from analysis (i.e. stimulus marks), since we do not spectrally or
  5. % otherwise separate tonic water or semale stimuli. It is possible to build a setup to always make these in the same place, and
  6. % thus automate this step, but it is also useful to have flexibility in where to pipette stimuli when an animal is moving
  7. % around. Running only this step on all videos first allows the more time-consuming urine detection across
  8. % all frames to be done unsupervised in batches.
  9. %
  10. % Author: Jason Keller
  11. % Date: June 2018
  12. %
  13. % please cite: Keller, Stowers et al, Nature Neuroscience, 2018
  14. %
  15. % INPUT:
  16. % [filepath]
  17. % [mouseNum]
  18. %
  19. % OUTPUT:
  20. % [eum] - mask with final urine spots to be counted, cropped; an overlay image is saved for simple quality control check
  21. %
  23. %% read video % select negative threshold to track mouse
  24. filename = [filepath, mouseNum, '.mp4']; %I used MP4 but any file format that VideoReader can handle is acceptable
  25. display(['making EUM, mouse ' mouseNum]);
  26. smufObj = VideoReader(filename);
  28. nFrames = smufObj.NumberOfFrames;
  29. % NOTE: parameters below must be updated in both "smufMakeEum" and "smufVideoToPixels"
  30. topCut = 5; %hard code to cut off black border for cropped video output (use makeMask.jpg to estimate)
  31. bottomCut = 350;
  32. leftCut = 24;
  33. rightCut = 590;
  35. vidHeight = bottomCut-topCut; %smufObj.Height;
  36. vidWidth = rightCut-leftCut; %smufObj.Width;
  37. % nTotalPixels = vidHeight*vidWidth;
  38. % frameRate = smufObj.FrameRate; %in fps;
  39. numFramesAvg = 3; %number of frames to avg; more is better for noise, less is better to capture last bit of urine
  41. %thresh parameters, depends on lighting and camera conditions:
  42. % NOTE: this should be updated to the same value both here and in smufVideoToPixels.m when changing conditions
  43. thresh = 175; %found using threshToolMod (needs uint8 input);
  45. %% Preallocate the movie matrix & read frames
  46. fullMov = zeros(vidHeight,vidWidth,3,numFramesAvg,'uint8'); %need full RGB saved to output results on top
  47. grMov = zeros(vidHeight,vidWidth,numFramesAvg,'uint8'); %use green + red channels since they have most information
  48. gPercent = 0.5; %red seems to counterbalance mouse shadow (light in green channel, dark in red channel)
  49. rPercent = 1 - gPercent;
  51. for k = 1:numFramesAvg %use last 3 frames for EUM; read one frame at a time:
  52. frameNum = nFrames-numFramesAvg+k;
  53. tempS = read(smufObj,frameNum);
  54. fullMov(:,:,:,k) = tempS(topCut:bottomCut-1, leftCut:rightCut-1,:); %read method returns a H-by-W-by-B-by-F matrix, video,where H is the image frame height, W isthe image frame width, B is the number of bandsin the image (for example, 3 for RGB), and F isthe number of frames read
  55. grMov(:,:,k) = squeeze(fullMov(:,:,1,k)*rPercent + fullMov(:,:,2,k)*gPercent);
  56. grMov(:,:,k) = imsharpen(grMov(:,:,k),'Radius',20,'Amount',3, 'Threshold', 0); %sharpen to accentuate urine edges; parameters found manually
  57. end
  59. % manually select exclusion pixels (e.g. stimulus, mouse, reflections)
  60. lastFrames = uint8(mean(grMov,numFramesAvg)); %use mean over time instead of max projection
  62. %% select exclusion spots
  63. hFig = figure;
  64. hIm = imagesc(lastFrames);
  65. axis off;
  66. set(gcf, 'Position', get(0,'Screensize')); % Maximize figure
  68. hDoneControl = uicontrol(hFig, 'Style', 'pushbutton', 'String', 'DONE',... %make button to press when done
  69. 'Callback', @doneCallback, 'Position', [50 50 100 20]); %#ok<NASGU>
  71. % User selects stimulus ROIs with mouse (or any other exclusion pixels):
  72. set(hFig, 'Name','Use mouse to circle urine exclusion areas, press DONE when finished');
  73. exitStim = false;
  74. exclude = logical(zeros(vidHeight,vidWidth)); %#ok<LOGL>
  75. while(~exitStim)
  76. hStimRoi = imfreehand(gca);
  77. exclude = exclude | createMask(hStimRoi,hIm); %OR the masks to combine
  78. end
  79. close(hFig);
  80. pause on; pause(0.1); pause off; %allow figure to close
  82. %% thresholding:
  83. % thresh = threshToolMod(lastFrames) %can uncomment here when first setting up
  84. BW = im2bw(lastFrames, thresh/255);
  85. eum = BW & cageMask(topCut:bottomCut-1, leftCut:rightCut-1) &~exclude;
  87. %% make overlay image for QC:
  88. urineDot = uint8([255 255 0]);
  89. overlay = zeros(vidHeight,vidWidth,'uint8');
  90. tempR = fullMov(:,:,1,end); %pull out current frame to allow linear indexing
  91. tempG = fullMov(:,:,2,end);
  92. tempB = fullMov(:,:,3,end);
  93. tempR(eum) = repmat(urineDot(1), length(find(eum)), 1); %set movie pixels for QC
  94. tempG(eum) = repmat(urineDot(2), length(find(eum)), 1);
  95. tempB(eum) = repmat(urineDot(3), length(find(eum)), 1);
  96. overlay(:,:,1) = tempR;
  97. overlay(:,:,2) = tempG;
  98. overlay(:,:,3) = tempB;
  99. figure; imagesc(overlay)
  100. filenameEum = [filepath, mouseNum, '_eumOverlay.jpg'];
  101. imwrite(overlay, filenameEum);
  103. %% callbacks
  104. function doneCallback(hObject, ~)
  105. delete(hObject);
  106. exitStim = true;
  107. end
  109. end %end function smufMakeEum

smufMakeEum.m at commit 83adab2, under GPL-3.0 · at the source

Overview

Authors: Sourish Mukhopadhyay1,2, Natalie Cole2, Pansée ElGhayati2,3, Anna Pallé2, Caitlin H. Miller2, David Melendez-Perdomo2,3, Jason A. Keller2, John P. Crimaldi4, Bard Ermentrout5, Lisa Stowers2,6
ORCID iDs: Caitlin H. Miller, Lisa Stowers
  1. Biomedical Sciences Graduate Program, Scripps Research, La Jolla, CA, USA
  2. Department of Neuroscience, Scripps Research, La Jolla, CA, USA
  3. University of California, San Diego, San Diego, CA, USA
  4. Department of Civil, Environmental & Architectural Engineering, University of Colorado, Boulder, CO, USA
  5. Department of Mathematics, University of Pittsburgh, Pittsburgh, PA, USA
  6. Lead contact
Institutions: Scripps Research Institute (United States); University of California San Diego (United States); University of Colorado Boulder (United States); University of Pittsburgh (United States)
Journal: Cell reports, volume 45, issue 6, article 117432
Dates: published online 22 May 2026; in print 23 June 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1016/j.celrep.2026.117432 · PMID 42176265 · PMCID PMC13505964 · OpenAlex W7162082538
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: mouse (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Evoked potentials
Keywords: Sex hormones, Pheromones, Estrogen, Social behavior, Neuroscience, Sex behavior, Sexual Dimorphism, chemical communication, Urinary Function, Scent Marking, Social Communication, Urine Marking, Cp: Neuroscience, Barringtons Nucleus
MeSH: Animal Communication*, Motivation*, Pheromones*, Sexual Behavior, Animal*, Social Behavior*, Animals, Estrogen Receptor alpha, Female, Male, Mice, Mice, Inbred C57BL, Neurons, Odorants (* major topic)
Topic: Neuroendocrine regulation and behavior (Endocrine and Autonomic Systems, Neuroscience), according to OpenAlex
Funding: National Science Foundation (DBI 2014217, IOS1556085, 2014217); NIDCD NIH HHS (R01 DC015253); national science foundation graduate research fellowship program (/ CIHR / DFG / FRQ /); NINDS NIH HHS (R01 NS108439); National Science Foundation Division of Graduate Education (DGE-1144086); Fonds de recherche du Québec; National Institutes of Health; National Institute on Deafness and Other Communication Disorders (R01DC015253); Canadian Institutes of Health Research; Deutsche Forschungsgemeinschaft
Citations: cited by 1 paper (Europe PMC); 80 references in the paper
Research resources: Alexa Fluor 488 Goat anti-Rabbit RRID:AB_143165, Rabbit anti-GFP antibody RRID:AB_221569, Ethovision XT RRID:SCR_000441, MATLAB RRID:SCR_001622, Prism RRID:SCR_002798, After Effects RRID:SCR_010279

Abstract

Many species communicate via pheromone signals that orchestrate key social and survival behaviors. In laboratory assays, only male mice are observed to broadcast pheromones through urine scent marking. This has contributed to the view that males have specialized circuits and anatomy to intentionally transmit urine pheromones and actively participate in socio-chemical communication, while females remain mute recipients in laboratory settings. Here, we find that simple modifications to standard assays reveal exuberant urine marking by laboratory females, enabling reexamination of its dimorphic features. Chemogenetic inhibition of estrogen receptor-1-expressing (Esr1) neurons in Barrington’s nucleus confirms that both sexes rely on a similar mechanistic strategy necessary for urine marking. Moreover, we find that males and females mark toward a broad set of receivers, including reproductively incapable partners. Sex parity in urine marking reframes the understanding of voluntary chemo-communication function beyond a male-specific behavior to a broader social communication strategy engaged independent of sex or reproductive status.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.

stowerslab/smuf

License: GPL-3.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 83adab2e6094a81a056123ce921f9cac0580ce90, 18 June 2018
Languages: MATLAB (9)
Size: 12 files, 9 scripts
Software Heritage: archived
Found in: “Data and code availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Image Processing Toolbox (2 files), boundedline (1 file), Statistics and Machine Learning Toolbox (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
11 files
At the source: github.com/stowerslab/smuf

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

Tracing map

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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;
  • 9 scripts, each with its path and the digest of its content;
  • 3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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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.

Data and code availability

All data that support the findings of this study are available from the corresponding author upon reasonable request.

All analysis codes were previously made available47 and can be found online at github.com/stowerslab/smuf.

Any additional information required to reproduce results and 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 2, 28 September 2026

  • Publisher: n/a → Cell Press
  • Authors: added Lisa Stowers (0000-0002-4403-1269); removed Lisa Stowers

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 14 keywords, 13 MeSH terms, 10 funders, 69 references, 6 RRIDs.

Cite

This paper

Mukhopadhyay, S., Cole, N., ElGhayati, P., Pallé, A., Miller, C. H., Melendez-Perdomo, D., Keller, J. A., Crimaldi, J. P., Ermentrout, B., & Stowers, L. (2026). Male and female mice scent mark during social communication regardless of sexual motivation or partner identity. Cell reports, 45(6), 117432. https://doi.org/10.1016/j.celrep.2026.117432

BibTeX

@article{mukhopadhyay2026male,
author = {Mukhopadhyay, Sourish and Cole, Natalie and ElGhayati, Pansée and Pallé, Anna and Miller, Caitlin H. and Melendez-Perdomo, David and Keller, Jason A. and Crimaldi, John P. and Ermentrout, Bard and Stowers, Lisa},
title = {{Male and female mice scent mark during social communication regardless of sexual motivation or partner identity}},
journal = {Cell reports},
year = {2026},
month = may,
volume = {45},
number = {6},
pages = {117432},
publisher = {Cell Press},
issn = {2211-1247},
doi = {10.1016/j.celrep.2026.117432},
url = {https://doi.org/10.1016/j.celrep.2026.117432},
pmid = {42176265},
pmcid = {PMC13505964}
}

RIS

TY - JOUR
AU - Mukhopadhyay, Sourish
AU - Cole, Natalie
AU - ElGhayati, Pansée
AU - Pallé, Anna
AU - Miller, Caitlin H.
AU - Melendez-Perdomo, David
AU - Keller, Jason A.
AU - Crimaldi, John P.
AU - Ermentrout, Bard
AU - Stowers, Lisa
TI - Male and female mice scent mark during social communication regardless of sexual motivation or partner identity
T2 - Cell reports
J2 - Cell Rep
PY - 2026
DA - 2026/05/22
VL - 45
IS - 6
SP - 117432
SN - 2211-1247
PB - Cell Press
DO - 10.1016/j.celrep.2026.117432
UR - https://doi.org/10.1016/j.celrep.2026.117432
LA - en
ER -

CSL-JSON

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"family": "Mukhopadhyay",
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