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Protocol for recording visual maps in the mouse superior colliculus and visual cortex with intrinsic optical imaging.

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Paper

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The authors' code

MATLAB · 66 lines · 2 KB · no license

  1. %% ========================================================================
  2. % Analysis_IOI.m
  3. % Intrinsic Optical Imaging pipeline:
  4. % 1) Normalize data
  5. % 2) Rearrange frames by cycle phase
  6. % 3) PCA + Indicator Function method
  7. % 4) Reconstruct cleaned data
  8. % 5) FFT retinotopy maps (phase + amplitude)
  9. % ========================================================================
  11. %% Parameters
  12. xdim = 204; ydim = 198;
  13. n_pixel = xdim * ydim;
  15. n_frame_total = 400; % Downsized for GitHub (orig 2400)
  16. n_cycle_total = 5; % Downsized cycles (orig 30)
  17. n_frame_per_cycle = n_frame_total / n_cycle_total;
  19. T = 0.1; % 100 ms sampling
  20. Fs = 1/T;
  21. Cycle = 8; % stimulus cycle (s)
  23. %% Load data (Data_IOI size is [n_frame_total x pixels])
  24. load Data_IOI
  26. %% Normalize each pixel by its temporal mean
  27. Data_IOI_normalized = zeros(size(Data_IOI));
  28. Data_IOI_mean = mean(Data_IOI,1);
  29. for frame=1:n_frame_total
  30. Data_IOI_normalized(frame,:) = Data_IOI(frame,:) ./ Data_IOI_mean;
  31. end
  33. %% Rearrange frames by cycle phase
  34. Data_IOI_reaarange = zeros(size(Data_IOI));
  35. for i = 1:n_frame_per_cycle
  36. dst = (1:n_cycle_total) + (i-1)*n_cycle_total;
  37. src = i:n_frame_per_cycle:n_frame_total;
  38. Data_IOI_reaarange(dst,:) = Data_IOI_normalized(src,:);
  39. end
  41. %% PCA + Indicator Function method
  42. [psi, a, ev] = pca(Data_IOI_reaarange);
  43. [phi, rho] = ind(psi, a, ev, n_frame_per_cycle, 4);
  44. Data_IOI_clean = rho * phi';
  46. %% Restore chronological order
  47. Data_IOI_result = zeros(size(Data_IOI));
  48. for i = 1:n_frame_per_cycle
  49. src = (1:n_cycle_total) + (i-1)*n_cycle_total;
  50. dst = i:n_frame_per_cycle:n_frame_total;
  51. Data_IOI_result(dst,:) = Data_IOI_clean(src,:);
  52. end
  54. %% FFT-based retinotopy maps
  55. NFFT = n_frame_per_cycle;
  56. freqs = (0:NFFT-1)*Fs/NFFT;
  57. [~, IDX] = min(abs(freqs - 1/Cycle));
  59. Y = fft(Data_IOI_result, NFFT)/NFFT;
  60. Yabs = 2 * abs(Y(1:NFFT/2,:));
  62. PHASE1 = -angle(Y(IDX,:));
  63. MAG1 = Yabs(IDX,:);
  65. MAG1 = reshape(MAG1, xdim, ydim).';
  66. PHASE1 = reshape(PHASE1,xdim, ydim).';

Analysis_IOI.m at commit d19fbf7, no license · at the source

Overview

Authors: Flora Boutet-Porretta1,2, Josien Visser1, Arthur Matthys1,2, Armelle Rancillac1, Nathalie Rouach1, Jérôme Ribot1
ORCID iDs: Flora Boutet-Porretta, Jérôme Ribot
  1. Center for Interdisciplinary Research in Biology, Collège de France, CNRS, INSERM, PSL-Neuro, Université PSL, Paris, France
  2. Doctoral School N°158, Sorbonne Université, Paris, France
Institutions: Centre National de la Recherche Scientifique (France); Inserm (France); Collège de France (France); Université Paris Sciences et Lettres (France); Sorbonne Université (France); Centre Interdisciplinaire de Recherche en Biologie (France)
Journal: STAR protocols, volume 7, issue 1, article 104430
Dates: published online 12 March 2026; in print March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.xpro.2026.104430 · PMID 41824446 · PMCID PMC12990355 · OpenAlex W7135067005
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), optical imaging (calcium, voltage, 2-photon) (modality), mouse (organism), systems (subfield)
Methods: Spectral & time-frequency, Evoked potentials, fMRI & imaging, Smoothing, state filtering, decompositions, Physiology & signal measures
Keywords: Microscopy, Cognitive Neuroscience, Systems biology
MeSH: Brain Mapping*, Optical Imaging*, Superior Colliculi*, Visual Cortex*, Animals, Mice (* major topic)
Topic: Photoreceptor and optogenetics research (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: Fondation de France; Fondation pour la Recherche Médicale (Foundation for Medical Research in France); European Research Council (683154); European Union’s Horizon 2020 research and innovation program (722053); Agence Nationale de la Recherche (French National Research Agency) (ANR-24-CHBS-0007, ANR-10-IDEX-0001); PSL Research University
Citations: cited by 1 paper (Europe PMC); 30 references in the paper
Research resources: RRID:IMSR_JAX:000664, MATLAB (Version r2023b) RRID:SCR_001622

Abstract

Intrinsic optical imaging (IOI) is a powerful approach to record visual-functional maps across the mouse superior colliculus (SC) and primary visual cortex (V1). Here, we present a protocol to map retinotopy and orientation preference in the SC within 15 min using periodic stimulation and Fourier analysis. We also describe how to obtain ocular dominance maps in V1 from independent monocular stimulation. We provide detailed instructions for surgical preparation, imaging setup, and preprocessing techniques.

For complete details on the use and execution of this protocol, please refer to Visser et al.1

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

Repositories

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

tchetch12/IOI_Retinotopy_Analysis

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: d19fbf75e01a3d8dc27e44901420607118f97664, 1 December 2025
Languages: MATLAB (3)
Size: 4 files, 3 scripts
Software Heritage: not archived
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 30 September 2026: the link answers
  • 30 September 2026: the link answers
3 files
At the source: github.com/tchetch12/IOI_Retinotopy_Analysis

Zenodo 18662251

License: CC-BY-4.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Languages: MATLAB (3)
Size: 4 files, 3 scripts
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
3 files
At the source:

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;
  • 6 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 and code availability

Example dataset (retinotopic maps from Figure 3) and all custom analysis code supporting this study have been deposited in GitHub at https://github.com/tchetch12/IOI_Retinotopy_Analysis.

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, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 3 keywords, 6 MeSH terms, 6 funders, 30 references, 2 RRIDs.

Cite

This paper

Boutet-Porretta, F., Visser, J., Matthys, A., Rancillac, A., Rouach, N., & Ribot, J. (2026). Protocol for recording visual maps in the mouse superior colliculus and visual cortex with intrinsic optical imaging. STAR protocols, 7(1), 104430. https://doi.org/10.1016/j.xpro.2026.104430

BibTeX

@article{boutetporretta2026protocol,
author = {Boutet-Porretta, Flora and Visser, Josien and Matthys, Arthur and Rancillac, Armelle and Rouach, Nathalie and Ribot, Jérôme},
title = {{Protocol for recording visual maps in the mouse superior colliculus and visual cortex with intrinsic optical imaging}},
journal = {STAR protocols},
year = {2026},
month = mar,
volume = {7},
number = {1},
pages = {104430},
publisher = {Elsevier},
issn = {2666-1667},
doi = {10.1016/j.xpro.2026.104430},
url = {https://doi.org/10.1016/j.xpro.2026.104430},
pmid = {41824446},
pmcid = {PMC12990355}
}

RIS

TY - JOUR
AU - Boutet-Porretta, Flora
AU - Visser, Josien
AU - Matthys, Arthur
AU - Rancillac, Armelle
AU - Rouach, Nathalie
AU - Ribot, Jérôme
TI - Protocol for recording visual maps in the mouse superior colliculus and visual cortex with intrinsic optical imaging
T2 - STAR protocols
J2 - STAR Protoc
PY - 2026
DA - 2026/03/12
VL - 7
IS - 1
SP - 104430
SN - 2666-1667
PB - Elsevier
DO - 10.1016/j.xpro.2026.104430
UR - https://doi.org/10.1016/j.xpro.2026.104430
LA - en
ER -

CSL-JSON

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