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Undoing of firing rate adaptation enables invariant population codes.

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Paper

Loaded from Europe PMC by your browser; OSCR does not store it: doi.org · Europe PMC

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The authors' code

MATLAB · 41 lines · 891 B · CC-BY-4.0

  1. function [] = Batch_Alignment()
  3. % reference image for allignment
  4. ref = 750;
  6. % Prompt for manual browse to image folder
  7. folder_name = uigetdir(pwd, 'Select Folder containing Prairie Images');
  9. if folder_name == 0
  10. error('no folder selected')
  11. end
  13. display(folder_name);
  15. files = dir([folder_name, '/TSeries*fly*']);
  17. dirFlags = [files.isdir];
  18. tseries = files(dirFlags);
  19. num_tseries = size(tseries,1);
  21. if num_tseries==0
  22. error('no TSeries available');
  23. else
  24. for i=1:num_tseries
  25. tic
  26. s = regexp(tseries(i).name, '.tif', 'split');
  27. if exist([folder_name, '/', s{1}, '_times.mat'],'file')~=2
  28. display(tseries(i).name);
  29. tseries_align([folder_name, '/', tseries(i).name], ref);
  30. else
  31. disp([tseries(i).name ' DONE']);
  32. end
  33. toc
  34. end
  35. end
  37. disp('all DONE');
  39. end

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

Overview

Authors: Sofia C. Brandão1, Luisa Ramirez1,2, Pascal Züfle1, Alexander M. Walter3, Marion Silies1,2, Carlotta Martelli1,2
ORCID iDs: Sofia C. Brandão, Luisa Ramirez, Pascal Züfle, Alexander M. Walter, Marion Silies, Carlotta Martelli
  1. Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Mainz, Germany
  2. Institute for Quantitative and Computational Biosciences (IQCB), Johannes Gutenberg University, Mainz, Germany
  3. Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Institutions: Johannes Gutenberg University Mainz (Germany); University of Copenhagen (Denmark)
Journal: Science advances, volume 12, issue 34, article eaeg3535
Dates: received 11 February 2026; accepted 10 July 2026; published online 19 August 2026; in print August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1126/sciadv.aeg3535 · PMID 42616897 · PMCID PMC13488935 · OpenAlex W4402910542
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2024.09.26.614457
Status: code verified (how the code is found and verified)
Categories: cellular / molecular (subfield)
Methods: Spectral & time-frequency, Smoothing, state filtering, decompositions, Single-unit activity, calcium imaging
MeSH: Action Potentials*, Adaptation, Physiological*, Olfactory Receptor Neurons*, Animals, Calcium, Models, Neurological, Odorants, Olfactory Pathways, Smell (* major topic)
Journal subjects: Neuroscience
Topic: Machine Learning in Bioinformatics (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: European Research Council (ERC Consolidator Grant AdapativeVision, grant agreement no. 101045003, ERC Consolidator Grant PlasticSite, grant agreement no. 101045054); Deutsche Forschungsgemeinschaft (MA7804/2-1, P4 FOR5289, P5 FOR5289); Novo Nordisk Fonden (Young Investigator Award NNF19OC0056047)
Citations: not cited yet (Europe PMC); 95 references in the paper

Abstract

Neural adaptation supports coding efficiency by tuning responses to prevailing stimulus statistics. However, when information is represented by populations of neurons, adaptation of individual units could degrade behaviorally relevant signals. Here, we investigate how the fly olfactory system implements adaptation to background odors in olfactory receptor neurons (ORNs) and the consequences for combinatorial coding in downstream circuits. We show that adaptation of ORN firing rate is compensated at the axon terminal, where inhibitory presynaptic feedback supports background-invariant calcium responses to increases (but not decreases) in odor concentration. Computational analyses demonstrate that such invariance requires an adaptation strategy in ORNs that shifts response amplitude rather than sensitivity, diverging from efficient coding principles in single neurons. Downstream, postsynaptic projection neurons also exhibit background-invariant responses through presynaptic plasticity involving Unc13 proteins. Thus, the olfactory circuit restores stable population codes by undoing peripheral firing rate adaptation, enabling an asymmetric contrast representation that preserves stimulus identity across backgrounds.

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 15937307

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 11 files
Software Heritage: not checked
Found in: “Data, code, and materials availability:”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
9 files
At the source: zenodo.org/records/15937307

gitlab.rlp.net/mrtlllab/brandao_ramirez_adaptation2024

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: a54df0013c5ac4886ab4959393bbcfb1a9bc3d6a, 17 July 2025
Languages: Jupyter (2)
Size: 3 files, 2 scripts
Software Heritage: not archived
Found in: “Data, code, and materials availability:”
Holds: README, 2 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Matplotlib (2 files), NumPy (2 files), SciPy (2 files), scikit-learn (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
3 files
At the source: gitlab.rlp.net/mrtlllab/brandao_ramirez_adaptation2024

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;
  • 11 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, code, and materials availability

All data and code needed to evaluate and reproduce the conclusions in the paper are present in the paper and/or the Supplementary Materials. Raw data, scripts, and software for data curation and analysis have been deposited in Zenodo and are accessible at https://zenodo.org/records/15937307. Additional resources for the computational model are available on GitHub: https://gitlab.rlp.net/mrtlllab/brandao_ramirez_adaptation2024.

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, issue, pages, dates, 6 authors, 9 MeSH terms, 3 funders, 91 references.

Cite

This paper

Brandão, S. C., Ramirez, L., Züfle, P., Walter, A. M., Silies, M., & Martelli, C. (2026). Undoing of firing rate adaptation enables invariant population codes. Science advances, 12(34), eaeg3535. https://doi.org/10.1126/sciadv.aeg3535

BibTeX

@article{brandao2026undoing,
author = {Brandão, Sofia C. and Ramirez, Luisa and Züfle, Pascal and Walter, Alexander M. and Silies, Marion and Martelli, Carlotta},
title = {{Undoing of firing rate adaptation enables invariant population codes}},
journal = {Science advances},
year = {2026},
month = aug,
volume = {12},
number = {34},
pages = {eaeg3535},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
doi = {10.1126/sciadv.aeg3535},
url = {https://doi.org/10.1126/sciadv.aeg3535},
pmid = {42616897},
pmcid = {PMC13488935}
}

RIS

TY - JOUR
AU - Brandão, Sofia C.
AU - Ramirez, Luisa
AU - Züfle, Pascal
AU - Walter, Alexander M.
AU - Silies, Marion
AU - Martelli, Carlotta
TI - Undoing of firing rate adaptation enables invariant population codes
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/08/19
VL - 12
IS - 34
SP - eaeg3535
SN - 2375-2548
PB - American Association for the Advancement of Science
DO - 10.1126/sciadv.aeg3535
UR - https://doi.org/10.1126/sciadv.aeg3535
LA - en
ER -

CSL-JSON

{
"id": "10.1126/sciadv.aeg3535",
"type": "article-journal",
"title": "Undoing of firing rate adaptation enables invariant population codes",
"container-title": "Science advances",
"author": [
{
"family": "Brandão",
"given": "Sofia C."
},
{
"family": "Ramirez",
"given": "Luisa"
},
{
"family": "Züfle",
"given": "Pascal"
},
{
"family": "Walter",
"given": "Alexander M."
},
{
"family": "Silies",
"given": "Marion"
},
{
"family": "Martelli",
"given": "Carlotta"
}
],
"container-title-short": "Sci Adv",
"volume": "12",
"issue": "34",
"page": "eaeg3535",
"DOI": "10.1126/sciadv.aeg3535",
"PMID": "42616897",
"PMCID": "PMC13488935",
"ISSN": "2375-2548",
"publisher": "American Association for the Advancement of Science",
"URL": "https://doi.org/10.1126/sciadv.aeg3535",
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
19
]
]
}
}

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