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Topographically organized dorsal raphe activity modulates forebrain sensory-motor representations and contributes to defensive behaviors.

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Paper

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The authors' code

MATLAB · 112 lines · 3.5 KB · no license

  1. % Fig1_2_S1_S3_S4 - Main batch analysis and figure generation script
  2. % Runs the full analysis pipeline and generates figures corresponding to
  3. % Figures 1, 2, S1, S3, and S4 of the manuscript.
  4. %
  5. % Outputs:
  6. % - A large set of analysis results saved to disk (MAT-file).
  7. % - A comprehensive collection of figures saved to disk.
  9. % Author: Kadir Mutlu
  10. % Address: Olav Kyrres gate 9, 7030 Trondheim, Norway
  11. % email: [email hidden]
  12. % Website: https://www.ntnu.edu/kavli
  13. %
  14. % Copyright (c) 2019, Kadir Mutlu
  16. %%% Generate the object used throughout the analysis pipeline.
  17. cel_onl = sam_fun.cel_onl_fun();
  18. %%% Save animal-level data
  19. sav_rec_all(cel_onl)
  20. %
  21. sav_ima_cal_all(cel_onl)
  22. %%% Save sample-level data
  23. sav_dat_sam(cel_onl)
  24. %%% Append synch parameters and tail-related metrics
  25. sta_ani = 1;
  26. app_syn_axo_all(cel_onl, sta_ani)
  27. %
  28. app_tai_all(cel_onl, sta_ani)
  29. %%% Preprocess calcium imaging data
  30. app_cel_log_pla_row_col_all(cel_onl, sta_ani)
  31. %
  32. det_per_bin_edg_all(cel_onl, sta_ani)
  33. %
  34. app_log_pla_icx_row_col_all(cel_onl, sta_ani)
  35. %
  36. app_som_log_pla_row_col_cel_all(cel_onl, sta_ani)
  37. %%% Append tail data and processed data
  38. app_tai_dat(cel_onl)
  39. %
  40. app_som(cel_onl)
  41. %%% Append clustering data
  42. app_gab_clu_cel_k_all(cel_onl)
  43. %%% Append sample-level tail data
  44. app_tai(cel_onl)
  45. %
  46. app_par_tai_cel_all(cel_onl)
  47. %%% Save figures
  48. sav_fig_ong_cel_all(cel_onl)
  49. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  50. sav_fig_inh_exc_sig(cel_onl)
  51. %
  52. sav_fig_pcc_dis(cel_onl)
  53. %
  54. sav_fig_clu_fid(cel_onl)
  55. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  56. sav_fig_cor_cor_den(cel_onl)
  57. %
  58. sav_fig_clu(cel_onl)
  59. %
  60. sav_fig_inh_exc_spa_all(cel_onl)
  61. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  62. sav_fig_res(cel_onl)
  63. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  64. sav_fig_pie(cel_onl)
  65. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  66. sav_fig_clu_fid(cel_onl)
  67. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  68. sav_fig_clu_map_cel(cel_onl)
  69. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  70. sav_fig_pie_k(cel_onl)
  71. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  72. sav_fig_n_cel(cel_onl)
  73. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  74. sav_fig_dff_ang(cel_onl)
  75. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  76. sav_fig_nta_win(cel_onl)
  77. %
  78. sav_fig_pro_mul(cel_onl)
  79. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  80. sav_fig_inh_exc_spa_two(cel_onl)
  81. %
  82. sav_fig_res_acc_mod(cel_onl)
  83. %
  84. sav_fig_mod_loc(cel_onl)
  85. %
  86. sav_fig_roi_con_all(cel_onl)
  87. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  88. sav_fig_pai_mod(cel_onl)
  89. %
  90. sav_fig_pve_cel(cel_onl)
  91. %
  92. sav_fig_tap_tai_not(cel_onl)
  93. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  94. sav_fig_pve_cel_tau(cel_onl)
  95. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  96. sav_fig_inh_exc_spa_bou_non(cel_onl)% fraction plot
  97. %
  98. sav_fig_clu_loc_sig(cel_onl)
  99. %
  100. sav_fig_per_pai_mod(cel_onl)
  101. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  102. sav_fig_hab(cel_onl)
  103. %
  104. sav_fig_rep_sup(cel_onl)
  105. %
  106. sav_fig_ttn_sca_all(cel_onl)
  107. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  108. sav_fig_inh_exc_spl(cel_onl)
  109. %
  110. sav_fig_pie(cel_onl)
  111. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  112. sav_fig_ccd_spl(cel_onl)

Fig1_2_S1_S3_S4.m at commit ed53c37, no license · at the source

Overview

Authors: Aytac Kadir Mutlu1, Bram Serneels1, Christoph Wiest1,2, Anh-Tuan Trinh1, Ricarda Bardenhewer1, Fabrizio Palumbo1, Oda Bjørnevik Frisvold1, Inger Kristine Fjeldskaar Aukrust1, Anna Maria Ostenrath1, Emre Yaksi1,3
ORCID iDs: Aytac Kadir Mutlu, Anh-Tuan Trinh, Fabrizio Palumbo, Inger Kristine Fjeldskaar Aukrust, Anna Maria Ostenrath, Emre Yaksi
  1. Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Olav Kyrres gata 9,Trondheim, Norway
  2. National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust,London, UK
  3. Koç University Research Center for Translational Medicine, Koç University School of Medicine,Istanbul, Turkey
Institutions: Norwegian University of Science and Technology (Norway); University College London Hospitals NHS Foundation Trust (United Kingdom); Koç University (Türkiye)
Journal: Nature communications, volume 17, issue 1, article 6243
Dates: received 13 March 2025; accepted 30 June 2026; published online 16 July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41467-026-75490-y · PMID 42463658 · PMCID PMC13376501 · OpenAlex W7168764455
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: zebrafish (organism)
Methods: Statistics, Machine learning, Smoothing, state filtering, decompositions, Evoked potentials, fMRI & imaging, Single-unit activity, calcium imaging
Keywords: Neural circuits, Sensory processing, Sensorimotor processing
MeSH: Behavior, Animal*, Dorsal Raphe Nucleus*, Prosencephalon*, Animals, Animals, Genetically Modified, Axons, Glutamate Decarboxylase, Locomotion, Male, Neurons, Zebrafish, Zebrafish Proteins (* major topic)
Topic: Zebrafish Biomedical Research Applications (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Norges Forskningsråd (Forskningsrådet) (314212)
Citations: cited by 1 paper (Europe PMC); 148 references in the paper

Abstract

The dorsal raphe nucleus (DRN) shapes behaviors including mood and motivation. The DRN contains molecularly distinct and topographically organized neurons that target specific forebrain regions. To understand how DRN neurons process sensory information, we investigated the spatiotemporal activity patterns of DRN neurons, DRN axons, and their forebrain targets in zebrafish. We found a remarkable topographic organization of ongoing activity and sensory-motor responses within the DRN. A subset of DRN neurons was driven by locomotion and sensory stimuli. Gad1-positive DRN neurons exhibited distinct activity during rest and sensory-motor stimulation. DRN axons in the forebrain showed topographically organized excitation and inhibition in response to sensory stimulation and locomotion. DRN axons covaried with forebrain neuronal activity. DRN ablation reduced the synchrony and sensory-motor responses of forebrain neurons and enhanced defensive behaviors. We revealed the functional diversity of DRN neurons and their role in transmitting sensory and locomotor signals via topographically organized forebrain projections.

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

Repositories

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

yaksilab/drn_paper

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: ed53c371d0baef5e05ece64650883cb0297354bd, 7 April 2026
Languages: MATLAB (818), C (14), C++ (5), C/C++ (5), Java (2)
Size: 1,101 files, 844 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, tests, documentation
Not found: license file, CITATION.cff, environment file, continuous integration
Tools: Statistics and Machine Learning Toolbox (105 files), boundedline (32 files), Signal Processing Toolbox (21 files), shadedErrorBar (16 files), export_fig (14 files), Image Processing Toolbox (14 files), Curve Fitting Toolbox (5 files), EEGLAB (4 files), Violinplot-Matlab (3 files), Parallel Computing Toolbox (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
845 files
At the source: github.com/yaksilab/drn_paper

Zenodo 19452784

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: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Statistics and Machine Learning Toolbox (105 files), boundedline (32 files), Signal Processing Toolbox (21 files), shadedErrorBar (16 files), export_fig (14 files), Image Processing Toolbox (14 files), Curve Fitting Toolbox (5 files), EEGLAB (4 files), Violinplot-Matlab (3 files), Parallel Computing Toolbox (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
845 files
At the source:

Code availability

Main associated codes that are used to make figures are available at: 10.5281/zenodo.19452784 and https://github.com/yaksilab/drn_paper.

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

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;
  • 1,688 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

Calcium imaging data reported in this paper have been deposited in the sigma2 data base under the accession code 10.11582/2026.93nyzmjx. Source data are provided with this paper as a Source Data file.

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, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 3 keywords, 12 MeSH terms, 1 funder, 139 references.

Cite

This paper

Mutlu, A. K., Serneels, B., Wiest, C., Trinh, A.-T., Bardenhewer, R., Palumbo, F., Frisvold, O. B., Aukrust, I. K. F., Ostenrath, A. M., & Yaksi, E. (2026). Topographically organized dorsal raphe activity modulates forebrain sensory-motor representations and contributes to defensive behaviors. Nature communications, 17(1), 6243. https://doi.org/10.1038/s41467-026-75490-y

BibTeX

@article{mutlu2026topographically,
author = {Mutlu, Aytac Kadir and Serneels, Bram and Wiest, Christoph and Trinh, Anh-Tuan and Bardenhewer, Ricarda and Palumbo, Fabrizio and Frisvold, Oda Bjørnevik and Aukrust, Inger Kristine Fjeldskaar and Ostenrath, Anna Maria and Yaksi, Emre},
title = {{Topographically organized dorsal raphe activity modulates forebrain sensory-motor representations and contributes to defensive behaviors}},
journal = {Nature communications},
year = {2026},
month = jul,
volume = {17},
number = {1},
pages = {6243},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-75490-y},
url = {https://doi.org/10.1038/s41467-026-75490-y},
pmid = {42463658},
pmcid = {PMC13376501}
}

RIS

TY - JOUR
AU - Mutlu, Aytac Kadir
AU - Serneels, Bram
AU - Wiest, Christoph
AU - Trinh, Anh-Tuan
AU - Bardenhewer, Ricarda
AU - Palumbo, Fabrizio
AU - Frisvold, Oda Bjørnevik
AU - Aukrust, Inger Kristine Fjeldskaar
AU - Ostenrath, Anna Maria
AU - Yaksi, Emre
TI - Topographically organized dorsal raphe activity modulates forebrain sensory-motor representations and contributes to defensive behaviors
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/07/16
VL - 17
IS - 1
SP - 6243
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-75490-y
UR - https://doi.org/10.1038/s41467-026-75490-y
LA - en
ER -

CSL-JSON

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