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A user-friendly graphical user interface for paw touch classification in rodent cylinder testing.

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Paper

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The authors' code

MATLAB · 72 lines · 3 KB · CC-BY-4.0

  1. % Define the target animal ID and files to analyze
  2. targetRatID = 'Rat1';
  3. targetFiles = {'TestGroupI.avi', 'TestGroupII.avi'};
  5. % Initialize counters
  6. touchCounts = struct('LeftWall', 0, 'RightWall', 0, 'BothWall', 0, ...
  7. 'LeftFloor', 0, 'RightFloor', 0);
  8. totalDuration = 0; % in seconds
  10. % Iterate through the DataNested structure
  11. for i = 1:numel(DataNested)
  12. % Check if the current file is in our target list
  13. if ismember(DataNested(i).Filename, targetFiles)
  15. % Find the subject matching our target ID
  16. subIdx = find(strcmp({DataNested(i).Subject.ID}, targetRatID));
  18. if ~isempty(subIdx)
  19. subjectData = DataNested(i).Subject(subIdx);
  21. % Iterate through all segments for this subject
  22. for segIdx = 1:numel(subjectData.Segment)
  23. currentSeg = subjectData.Segment(segIdx);
  25. % Calculate segment duration (Stop Time - Start Time)
  26. % Note: To calculate metrics for a *single* segment, you can
  27. % replace this loop by indexing a specific segIdx (e.g., segIdx = 1)
  28. segDuration = currentSeg.TimeRange(2) - currentSeg.TimeRange(1);
  29. totalDuration = totalDuration + segDuration;
  31. % Tally the touches within this segment
  32. for tIdx = 1:numel(currentSeg.Touch)
  33. touchType = currentSeg.Touch(tIdx).Touch;
  35. switch touchType
  36. case 'Left Wall'
  37. touchCounts.LeftWall = touchCounts.LeftWall + 1;
  38. case 'Right Wall'
  39. touchCounts.RightWall = touchCounts.RightWall + 1;
  40. case 'Both Wall'
  41. touchCounts.BothWall = touchCounts.BothWall + 1;
  42. case 'Left Floor'
  43. touchCounts.LeftFloor = touchCounts.LeftFloor + 1;
  44. case 'Right Floor'
  45. touchCounts.RightFloor = touchCounts.RightFloor + 1;
  46. end
  47. end
  48. end
  49. end
  50. end
  51. end
  53. % Calculate Key Metrics
  54. totalWallTouches = touchCounts.LeftWall + touchCounts.RightWall + touchCounts.BothWall;
  56. % Asymmetry Index: (Right - Left) / Total Wall Touches
  57. if totalWallTouches > 0
  58. asymmetryIndex = (touchCounts.RightWall - touchCounts.LeftWall) / totalWallTouches;
  59. else
  60. asymmetryIndex = NaN; % Prevent division by zero if no wall touches occurred
  61. end
  63. % Touch Rate: Total Wall Touches per minute
  64. touchRatePerMin = totalWallTouches / (totalDuration / 60);
  66. % Display Results
  67. fprintf('--- Results for %s ---\n', targetRatID);
  68. fprintf('Total Wall Touches: %d\n', totalWallTouches);
  69. fprintf('Asymmetry Index: %.2f\n', asymmetryIndex);
  70. fprintf('Total Time in Cylinder: %.1f seconds\n', totalDuration);
  71. fprintf('Rate of Wall Touches: %.2f touches/minute\n', touchRatePerMin);

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

Overview

Authors: Tyler R. Johnson1,2,3, Katherine D. Zerefos1,4, Dawn M. Taylor1,2,3
  1. Department of Neurosciences, Cleveland Clinic Research, The Cleveland Clinic, Cleveland, OH, United States
  2. Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
  3. Cleveland Functional Electrical Stimulation Center of Excellence, Louis Stokes Cleveland VA Medical Center, Cleveland, OH, United States
  4. Department of Neurosciences, Case Western Reserve University, Cleveland, OH, United States
Institutions: Cleveland Clinic (United States); Louis Stokes Cleveland VA Medical Center (United States); Case Western Reserve University (United States)
Journal: Frontiers in neuroscience, volume 20, article 1803569
Dates: received 4 February 2026; accepted 10 July 2026; published online 3 August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.3389/fnins.2026.1803569 · PMID 42609477 · PMCID PMC13478297 · OpenAlex W7172352880
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: Parkinson's (population), methods / tools (subfield)
Keywords: 6-hydroxydopamine (6-OHDA), cylinder test, forelimb asymmetry, hemiplegia, neuroscience education, paw-touch classification, rodent video analysis software, The Ratalyzer
Journal subjects: Technology and Code
Topic: Animal testing and alternatives (Small Animals, Veterinary), according to OpenAlex
Funding: RRD VA (I21 RX003592)
Citations: not cited yet (Europe PMC); 22 references in the paper

Abstract

In unilateral rodent models of disease or injury, deficits are induced in only one side of the body, allowing the difference in right versus left limb usage to serve as a metric of disease/injury severity and recovery with various treatments. Unilateral rat models are commonly used for conditions such as Parkinson’s disease (via the neurotoxin 6-hydroxydopamine, 6-OHDA), stroke, and traumatic brain injury, as well as cervical spinal cord injury and peripheral nerve damage. The ‘cylinder test’ has been used for over two decades as a reliable metric of asymmetry in forelimb usage. In this test, videos are taken of the rodent in a vertical cylinder as it explores its surroundings. The experimenter then logs which forepaw was used to first touch the cylinder wall each time the animal reared up on its hind limbs to start a new wall exploration sequence. The process of manually scanning through videos and logging left/right paw touches can be very time consuming and prone to errors. To streamline this process, we made The Ratalyzer, an easy-to-use graphical user interface (GUI) that: (1) facilitates efficiently moving through videos to find each initial wall touch event, (2) blinds the assessor to the animal and treatment state, and (3) electronically logs the paw-touch event type and time with just a push of a button thus eliminating error-prone paper notes or manual data entry. We are making this useful software tool available to the research community as both a compiled stand-alone program and as open-source MATLAB code. This tool could be useful for both researchers and educators, as analyzing cylinder-test videos via this GUI is a great way to engage high school and undergraduate students in performing neuroscience research without the risks and costs associated with making live animals available to students for hands-on testing.

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

Repositories

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

Zenodo 15750960

License: CC-BY-4.0
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data availability statement”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers (HTTP 200)
  • 26 September 2026: the link answers (HTTP 200)
1 file
At the source: doi.org/10.5281/zenodo.15750960

tyjo22/a-user-friendly-gui-for-paw-touch-classification-in-rodent-cylinder-testing

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: cd5f7460f81a378c8199e16b88ecf3604916426e, 1 April 2026
Languages: MATLAB (1)
Size: 9 files, 1 script
Software Heritage: not archived
Found in: the Zenodo archive record
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
1 file
At the source: github.com/TyJo22/A-User-Friendly-GUI-For-Paw-Touch-Classification-In-Rodent-Cylinder-Testing/tree/V_1.0

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 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.

Data availability statement

Publicly available datasets were analyzed in this study. The Ratalyzer program as well as all code used to make the program can be found at: https://doi.org/10.5281/zenodo.15750960.

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

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 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 3 authors, 8 keywords, 1 funder, 22 references.

Cite

This paper

Johnson, T. R., Zerefos, K. D., & Taylor, D. M. (2026). A user-friendly graphical user interface for paw touch classification in rodent cylinder testing. Frontiers in neuroscience, 20, 1803569. https://doi.org/10.3389/fnins.2026.1803569

BibTeX

@article{johnson2026user,
author = {Johnson, Tyler R. and Zerefos, Katherine D. and Taylor, Dawn M.},
title = {{A user-friendly graphical user interface for paw touch classification in rodent cylinder testing}},
journal = {Frontiers in neuroscience},
year = {2026},
month = aug,
volume = {20},
pages = {1803569},
publisher = {Frontiers Media SA},
issn = {1662-4548},
doi = {10.3389/fnins.2026.1803569},
url = {https://doi.org/10.3389/fnins.2026.1803569},
pmid = {42609477},
pmcid = {PMC13478297}
}

RIS

TY - JOUR
AU - Johnson, Tyler R.
AU - Zerefos, Katherine D.
AU - Taylor, Dawn M.
TI - A user-friendly graphical user interface for paw touch classification in rodent cylinder testing
T2 - Frontiers in neuroscience
J2 - Front Neurosci
PY - 2026
DA - 2026/08/03
VL - 20
SP - 1803569
SN - 1662-4548
PB - Frontiers Media SA
DO - 10.3389/fnins.2026.1803569
UR - https://doi.org/10.3389/fnins.2026.1803569
LA - en
ER -

CSL-JSON

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"container-title": "Frontiers in neuroscience",
"author": [
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"family": "Johnson",
"given": "Tyler R."
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"given": "Dawn M."
}
],
"container-title-short": "Front Neurosci",
"volume": "20",
"page": "1803569",
"DOI": "10.3389/fnins.2026.1803569",
"PMID": "42609477",
"PMCID": "PMC13478297",
"ISSN": "1662-4548",
"publisher": "Frontiers Media SA",
"URL": "https://doi.org/10.3389/fnins.2026.1803569",
"language": "en",
"issued": {
"date-parts": [
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