Rod photoreceptors have a dual dependency on both aerobic glycolysis and OXPHOS and diverge metabolically from other retinal neurons

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Paper

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The authors' code

MATLAB · 14 lines · 752 B · CC-BY-4.0

function [conf] = DFFanalysisConfig()
%% Input/output options %%
conf.chipsPath = 'M:\_Group\Software\CHIPS\CHIPS-finc\'; % Full path to the CHIPS library
conf.DFFanalysisPath = 'M:\Luca\MatlabCode\DFFanalysis\_DFFAnalysis'; % Path to the main FRETanalysis folder (the one containing the core code)
conf.tableFilePath = 'M:\Luca\MatlabCode\DFFanalysis\User\filesToProcess.xlsx'; % Full path to the input file
conf.filesDriveLetter = 'M:'; % Options: Tiff, ZeissZen
conf.outName = 'Test'; % Name of the current analysis (i.e. name of the subdir in Results)
%% ANYTHING BELOW THIS LINE IS FOR INTERNAL WORKING OF THE CODE. DO NOT CHANGE!
conf.configPath = strcat(mfilename('fullpath'), '.m');
end

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

Overview

Authors: Gabriele M. Wögenstein¹, Luca Ravotto², Vyara Todorova¹, Rachel M. Meister², Marijana Samardzija¹, L. Felipe Barros^3,4, Bruno Weber², Christian Grimm¹

ORCID iDs: Gabriele M. Wögenstein, Luca Ravotto, Rachel M. Meister, L. Felipe Barros, Christian Grimm

Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, Wagistrasse 14, Schlieren, 8952, Zurich, Switzerland
Institute of Pharmacology and Toxicology and Neuroscience Center Zurich, University and ETH Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland
Centro de Estudios Cientificos-CECs, Valdivia, Chile
Facultad de Medicina, Universidad San Sebastián, Valdivia, Chile

Journal: Science advances, volume 12, issue 41, article eaeg8687

Dates: received 2 March 2026; accepted 31 August 2026; published online 7 October 2026; in print October 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI · PMCID PMC13644791

Status: code verified (how the code is found and verified)

Categories: cellular / molecular (subfield)

Methods: Statistics, Connectivity, fMRI & imaging, Single-unit activity, calcium imaging, Physiology & signal measures

Journal subjects: Biomedicine and Life Sciences, Cell Biology, Cellular Neuroscience

Funding: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF) (310030_200798, 212508, 219656, 10006601); Hermann Kurz Foundation; Gudrun-Ulrika Foundation; Agencia Nacional de Investigación y Desarrollo (1230145)

Citations: not cited yet (Europe PMC); 102 references in the paper

Abstract

The retina metabolizes glucose into lactate, a hallmark of aerobic glycolysis known as the Warburg effect. Although evidence points to rod photoreceptors as the primary source of aerobic glycolysis, a comparison of the energy metabolism in different retinal neurons has yet to be performed. We combined two-photon fluorescence lifetime imaging of biosensors with pharmacological protocols to analyze metabolic dynamics in healthy and diseased rod photoreceptors and RBPMS-positive ganglion and calretinin-positive amacrine cells. Our data reveal distinct metabolic profiles among retinal neurons, identify rods as the drivers of aerobic glycolysis, demonstrate that inner retinal neurons rely on oxidative phosphorylation, show that rods need both glycolysis and oxidative phosphorylation to maintain ATP levels, and suggest that rods can metabolize lactate. A mutation causing retinitis pigmentosa increases lactate production in rods but changes the energy metabolism only subtly otherwise. Our results improve the understanding of retinal physiology and are relevant for pathologies involving imbalanced energy metabolism.

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

Repositories

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

doi:10.5061/dryad.gxd25482w

License: none: the authors keep all their rights

State: the link answers, verified on 9 October 2026

Evidence: the link answers

Software Heritage: not checked

Found in: “Data, code, and materials availability:”

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Availability: 1 check, the latest on 9 October 2026: the link answers (HTTP 200)

9 October 2026: the link answers (HTTP 200)

At the source: doi.org/10.5061/dryad.gxd25482w

Zenodo 22768263

License: CC-BY-4.0

State: the link answers, verified on 9 October 2026

Evidence: files inventoried

Size: 2 files

Software Heritage: not checked

Found in: the Zenodo software companion of the Dryad dataset

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Image Processing Toolbox (3 files), Statistics and Machine Learning Toolbox (3 files)

Availability: 1 check, the latest on 9 October 2026: the link answers (HTTP 200)

9 October 2026: the link answers (HTTP 200)

58 files

dffanalysis-master_(1).zip/dffanalysis-master/User/DFFanalysisConfig.m, MATLAB, 14 lines
dffanalysis-master_(1).zip/dffanalysis-master/User/DFFanalysisRun.m, MATLAB, 14 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/IntWeightRGB8.m, MATLAB, 116 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/addFloat32frame.m, MATLAB, 42 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/addRGB.m, MATLAB, 38 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/addUint16frame.m, MATLAB, 42 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/addUint8frame.m, MATLAB, 37 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/addWeightedRGB.m, MATLAB, 73 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/advancedColormap.m, MATLAB, 1,319 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/arrayFromXlsUnderscore.m, MATLAB, 12 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfCheckJavaMemory.m, MATLAB, 54 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfCheckJavaPath.m, MATLAB, 83 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfGetFileExtensions.m, MATLAB, 63 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfGetPlane.m, MATLAB, 95 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfGetPlaneAtZCT.m, MATLAB, 63 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfGetReader.m, MATLAB, 85 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfInitLogging.m, MATLAB, 45 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfOpen3DVolume.m, MATLAB, 54 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfTestInRange.m, MATLAB, 51 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfUpgradeCheck.m, MATLAB, 66 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfopen.m, MATLAB, 226 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/bfsave.m, MATLAB, 155 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/createMinimalOMEXMLMetadata.m, MATLAB, 99 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/bfmatlab/private/is_octave.m, MATLAB, 3 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/checkIfExistsOrIncrement.m, MATLAB, 25 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/checkNormalizationInterval.m, MATLAB, 18 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/deleteXlsSheets.m, MATLAB, 55 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/findLiThresholdValue.m, MATLAB, 181 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/gaussSmoothImages.m, MATLAB, 9 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/getNeighbours.m, MATLAB, 55 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/importTiffdata.m, MATLAB, 69 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/importZeissZenData.m, MATLAB, 51 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/makeDummyCHIPSarray.m, MATLAB, 22 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/makeDummyCalibration.m, MATLAB, 27 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/makeFullFrameTrace.m, MATLAB, 20 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/makeOutdirs.m, MATLAB, 22 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/makeROITables.m, MATLAB, 67 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/makeTimeScale.m, MATLAB, 30 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/motionCorrectImages.m, MATLAB, 21 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/printAnalysisSteps.m, MATLAB, 59 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/printColorBarInfos.m, MATLAB, 48 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/printDFFimages.m, MATLAB, 54 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/printMask.m, MATLAB, 9 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/printSingleDFFimages.m, MATLAB, 56 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/printTrace.m, MATLAB, 40 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/ratioThreshold.m, MATLAB, 14 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/readExpsFromXLS.m, MATLAB, 193 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/resizeImages.m, MATLAB, 18 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/threshChastagnierMask.m, MATLAB, 33 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/threshLiMask.m, MATLAB, 16 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/threshMaxValMask.m, MATLAB, 16 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/threshMinValMask.m, MATLAB, 15 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/threshOtsuMask.m, MATLAB, 17 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/timeBinImages.m, MATLAB, 36 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/timeSmoothImages.m, MATLAB, 8 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/turnInfsToNans.m, MATLAB, 8 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/core/updateNameNumbering.m, MATLAB, 48 lines
dffanalysis-master_(1).zip/dffanalysis-master/_DFFAnalysis/fDFFanalysisRun.m, MATLAB, 251 lines

At the source: zenodo.org/records/22768263

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.

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2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
58 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 results in the paper are present in the paper and/or the Supplementary Materials. To reproduce the results, all data and code are available on the Dryad repository associated with this project (https://doi.org/10.5061/dryad.gxd25482w). New viruses were generated by the VVF of the University of Zurich to express the different sensors in the different cell classes as described in the Materials and Methods (section “Cloning and virus production”). To request aliquots of the rod-specific viruses contact the corresponding author (). To order aliquots of the viruses used to transduce inner retina neurons contact the VVF of the University of Zurich (). Beyond virus production and data generation, no new material was generated.

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, 9 October 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 4 funders, 97 references.

Cite

This paper

Wögenstein, G. M., Ravotto, L., Todorova, V., Meister, R. M., Samardzija, M., Barros, L. F., Weber, B., & Grimm, C. (2026). Rod photoreceptors have a dual dependency on both aerobic glycolysis and OXPHOS and diverge metabolically from other retinal neurons. Science advances, 12(41), eaeg8687.

BibTeX

@article{wogenstein2026rod, author = {Wögenstein, Gabriele M. and Ravotto, Luca and Todorova, Vyara and Meister, Rachel M. and Samardzija, Marijana and Barros, L. Felipe and Weber, Bruno and Grimm, Christian}, title = {{Rod photoreceptors have a dual dependency on both aerobic glycolysis and OXPHOS and diverge metabolically from other retinal neurons}}, journal = {Science advances}, year = {2026}, month = oct, volume = {12}, number = {41}, pages = {eaeg8687}, publisher = {American Association for the Advancement of Science}, issn = {2375-2548}, pmcid = {PMC13644791} }

RIS

TY - JOUR AU - Wögenstein, Gabriele M. AU - Ravotto, Luca AU - Todorova, Vyara AU - Meister, Rachel M. AU - Samardzija, Marijana AU - Barros, L. Felipe AU - Weber, Bruno AU - Grimm, Christian TI - Rod photoreceptors have a dual dependency on both aerobic glycolysis and OXPHOS and diverge metabolically from other retinal neurons T2 - Science advances J2 - Sci Adv PY - 2026 DA - 2026/10/09 VL - 12 IS - 41 SP - eaeg8687 SN - 2375-2548 PB - American Association for the Advancement of Science LA - en ER -

CSL-JSON

{ "id": "pmcid:PMC13644791", "type": "article-journal", "title": "Rod photoreceptors have a dual dependency on both aerobic glycolysis and OXPHOS and diverge metabolically from other retinal neurons", "container-title": "Science advances", "author": [ { "family": "Wögenstein", "given": "Gabriele M." }, { "family": "Ravotto", "given": "Luca" }, { "family": "Todorova", "given": "Vyara" }, { "family": "Meister", "given": "Rachel M." }, { "family": "Samardzija", "given": "Marijana" }, { "family": "Barros", "given": "L. Felipe" }, { "family": "Weber", "given": "Bruno" }, { "family": "Grimm", "given": "Christian" } ], "container-title-short": "Sci Adv", "volume": "12", "issue": "41", "page": "eaeg8687", "PMCID": "PMC13644791", "ISSN": "2375-2548", "publisher": "American Association for the Advancement of Science", "language": "en", "issued": { "date-parts": [ [ 2026, 10, 9 ] ] } }

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