optical imaging (calcium, voltage, 2-photon)

Modality: 60 papers with a page, 45 of them with their authors' code.

Friday, 25 September 2026 (1 paper)

[1] Code ↔ Paper doi: [paper, repository]

Real-time closed-loop feedback system for mouse mesoscale cortical signal and movement control

Journal: eLife

Authors' code: pankajkgupta/clopy (GPL-3.0)

Status: code verified, 15 files readable, 11 matches

Thursday, 10 September 2026 (1 paper)

[2] doi:10.1162/imag.a.1357 [paper]

Biphasic acclimation for simultaneous wide-field fluorescent Ca<sup>2+</sup> imaging and fMRI of awake mice.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: code on request

Friday, 21 August 2026 (1 paper)

[3] Code ↔ Paper doi:10.3389/fncel.2026.1850197 [paper, repository]

Reward contingency reorganizes lateral orbitofrontal cortex pyramidal neuron activity from reward-aligned to action-aligned during associative learning.

Journal: Frontiers in cellular neuroscience

Authors' code: zichengyang/imaging_behavior (MIT)

Status: code verified, 7 files readable

Wednesday, 19 August 2026 (1 paper)

[4] doi:10.1073/pnas.2610398123 [paper, data]

Perceptual and neural constraints on photometric measures of heterochromatic brightness.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Status: data only, 1 dataset cited

Friday, 14 August 2026 (3 papers)

[5] Code ↔ Paper doi:10.1016/j.celrep.2026.117852 [paper, repository]

Graph theory identifies altered prefrontal microcircuit organization in Shank3 mice, a mouse Model of autism.

Journal: Cell reports

Authors' code: Zenodo 21490732 (CC-BY-4.0), liang-bo/AutoStereota (MIT)

Status: code verified, 62 files readable, 4 matches

[6] Code ↔ Paper doi:10.1038/s41592-026-03179-7 [paper, repository]

Voltage imaging of neurons distributed across entire brains of larval zebrafish.

Journal: Nature methods

Authors' code: Zenodo 14920628 (CC-BY-4.0)

Status: code verified, 4 files readable, 1 match

[7] Code ↔ Paper doi:10.1016/j.isci.2026.117212 [paper, repository]

Critical neuronal avalanches arise from excitation-inhibition balanced spontaneous activity.

Journal: iScience

Authors' code: adrianponce/ExcInh_Neuronal_Avalanches (no license)

Status: code verified, 8 files readable, 8 matches

Wednesday, 12 August 2026 (1 paper)

[8] doi:10.1117/1.jbo.31.8.086005 [paper]

Label-free wide-field imaging of brain tumors using near-infrared endogenous fluorescence and reflectance normalization.

Journal: Journal of biomedical optics

Status: code on request

Saturday, 8 August 2026 (1 paper)

[9] Code ↔ Paper doi:10.1016/j.isci.2026.117088 [paper, repository]

Spatial biases in visual feature representation of mouse dorsal lateral geniculate nucleus boutons.

Journal: iScience

Authors' code: Swamylab/Cha_et_al_Mouse_dLGN_FeatureMaps (no license), davidcsterratt/retistruct (no license)

Status: code verified, 131 files readable, 4 matches

Tuesday, 4 August 2026 (1 paper)

[10] Code ↔ Paper doi:10.21203/rs.3.rs-10218667/v1 [paper, repository]

Combining ultra-flexible electrodes with two-photon imaging to illuminate brain-wide neural dynamics

Journal: Research Square (preprint)

Authors' code: bichanw/RRR (no license)

Status: code verified, 18 files readable, 2 matches

Monday, 3 August 2026 (1 paper)

[11] Code ↔ Paper doi:10.1038/s41593-026-02350-9 [paper, repository]

Probing inter-areal computations with a two-photon holographic mesoscope.

Journal: Nature neuroscience

Authors' code: mesoholo/mesoholo (no license)

Status: code verified, 102 files readable, 8 matches

Saturday, 1 August 2026 (2 papers)

[12] Code ↔ Paper doi:10.1002/glia.70181 [paper, repository]

Female Mice Show Stronger Time-of-Day Modulation of Astrocytic Ca<sup>2+</sup> Activity in the Sleep-Regulatory Ventrolateral Preoptic Nucleus.

Journal: Glia

Authors' code: louzonca/AstroNet (CC0-1.0)

Status: code verified, 16 files readable, 2 matches

[13] Code ↔ Paper doi:10.1016/j.isci.2026.117010 [paper, repository]

Deep learning-assisted mapping of dendritic spines using sequential 2D two-photon calcium imaging.

Journal: iScience

Authors' code: dcupolillo/ROIpy (MIT), Zenodo 21334250 (MIT), dcupolillo/spyne (no license), Zenodo 21334656 (CC-BY-4.0), dcupolillo/calcium_event_classifier (no license), Zenodo 21334890 (CC-BY-4.0)

Status: code verified, 182 files readable, 21 matches

Thursday, 30 July 2026 (1 paper)

[14] Code ↔ Paper doi:10.1002/adhm.202503457 [paper, repository]

A 3D Human Neuron-on-Chip Platform to Monitor Neuronal Injury Responses.

Journal: Advanced healthcare materials

Authors' code: Thorowen/Calcium-imaging-data-processing (no license)

Status: code verified, 4 files readable, 3 matches

Friday, 24 July 2026 (1 paper)

[15] Code ↔ Paper doi:10.3390/biomedicines14081670 [paper, repository]

Limited Detectability of Network Functional Alterations in a Tauopathy Model Using Mouse Primary Cortical Cultures.

Journal: Biomedicines

Authors' code: Zenodo 1119025 (MIT)

Status: code verified, 949 files readable, 3 matches

Wednesday, 22 July 2026 (1 paper)

[16] Code ↔ Paper doi:10.1371/journal.pcbi.1013441 [paper, repository]

Large vision model framework for automated C. elegans analysis: From static morphometry to dynamic neural activity.

Journal: PLoS computational biology

Authors' code: lillyguisnet/TWARDISv0.1 (MIT), huggingface.co/lillyguisnet/celegans-classifier-vit-h-14-finetuned (no license)

Status: code verified, 19 files readable, 13 matches

Wednesday, 15 July 2026 (1 paper)

[17] Code ↔ Paper doi:10.1038/s41592-026-03154-2 [paper, repository]

Simultaneous single-cell calcium imaging of neuronal population activity and brain-wide BOLD fMRI.

Journal: Nature methods

Authors' code: rlemubaghs/camri (no license)

Status: code verified, 160 files readable, 11 matches

Tuesday, 14 July 2026 (1 paper)

[18] Code ↔ Paper doi:10.1002/advs.202515913 [paper, repository]

Intravital Multimodal Imaging of Human Cortical Organoid Transplantation in a Mouse Model of Chronic Stroke.

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Authors' code: liangy10/MIPOT (no license)

Status: empty repository, 1 file readable

Friday, 3 July 2026 (2 papers)

[19] doi:10.1038/s41377-026-02395-2 [paper, data]

Two-photon 3D imaging of optically stimulated neural activity at 100 Hz.

Journal: Light, science & applications

Status: data only, 2 datasets cited

[20] Code ↔ Paper doi:10.7554/elife.109240 [paper, repository]

Neural activity profiles reveal overlapping, intermingled subpopulations spanning area borders in mouse sensorimotor cortex.

Journal: eLife

Authors' code: kaufmanlab/SGK26-public (CC0-1.0)

Status: code verified, 132 files readable, 24 matches

Thursday, 2 July 2026 (1 paper)

[21] Code ↔ Paper doi:10.1016/j.xpro.2026.104678 [paper, repository]

Protocol for longitudinal two-photon calcium imaging and holographic optogenetic manipulation to investigate memory in mice.

Journal: STAR protocols

Authors' code: Zenodo 16830880 (GPL-3.0), ariadneunsworth/findusn (GPL-3.0)

Status: code verified, 228 files readable, 2 matches

Wednesday, 1 July 2026 (3 papers)

[22] Code ↔ Paper doi:10.1038/s41467-026-74834-y [paper, repository]

Voltage imaging of CA1 pyramidal cells and SST+ interneurons reveals stability and plasticity mechanisms of spatial firing.

Journal: Nature communications

Authors' code: yoavadamlab (no license)

Status: code verified

[23] Code ↔ Paper doi:10.1117/1.nph.13.3.035007 [paper, repository]

Analytical model enabling the correction of absorption and scattering in dual-color ratiometric multiphoton microscopy of brain tissue.

Journal: Neurophotonics

Authors' code: laboratory-charpak/Multiphoton-Ratiometric-Measurements-Model (MIT)

Status: code verified, 21 files readable

[24] doi:10.1117/1.nph.13.3.035008 [paper]

Metabolism and oxygen tension in Alzheimer's disease mouse model using two-photon FLIM-PLIM microscopy.

Journal: Neurophotonics

Status: code on request

Monday, 29 June 2026 (1 paper)

[25] doi:10.1186/s13020-026-01446-5 [paper, data]

The IL-17A modulating astrocytic activity was associated with the electroacupuncture-mediated improvement of sensorimotor ability after stroke.

Journal: Chinese medicine

Status: data only, 4 datasets cited

Thursday, 25 June 2026 (2 papers)

[26] Code ↔ Paper doi:10.1016/j.xpro.2026.104659 [paper, repository]

Protocol for simultaneous in vivo two-photon imaging and locomotion quantification during olfactory stimulation and pharmacology in walking Drosophila.

Journal: STAR protocols

Authors' code: SunLabWestlake/cia (no license)

Status: code verified, 9 files readable, 2 matches

[27] doi:10.1016/j.jneumeth.2026.110839 [paper, data]

Methods for measuring neural activity during voluntary wheel running.

Journal: Journal of neuroscience methods

Status: data only, 1 dataset cited

Monday, 22 June 2026 (1 paper)

[28] Code ↔ Paper doi:10.1038/s41592-026-03111-z [paper, repository]

A cloud-based miniscope for neurosurveillance of brain health and disease in freely behaving animals.

Journal: Nature methods

Authors' code: codeocean:4182092 (no license)

Status: code found, not verified yet

Thursday, 18 June 2026 (1 paper)

[29] Code ↔ Paper doi:10.1016/j.molmet.2026.102403 [paper, repository]

The central amygdala gates exogenous glucagon-like peptide 1 signals.

Journal: Molecular metabolism

Authors' code: OpenBehavior/Modular-Stereotaxic-Holders (GPL-3.0), Hardaway-Lab/FED3-Photometry_Workflows (no license)

Status: code verified, 16 files readable, 1 match

Wednesday, 17 June 2026 (1 paper)

[30] Code ↔ Paper doi:10.1364/boe.600665 [paper, repository]

NeuroSeg-MF: robust neuron segmentation in two-photon Ca<sup>2+</sup> imaging using multi-feature fusion and detection-guided SAM.

Journal: Biomedical optics express

Authors' code: XZH-James/NeuroSeg-MF (no license)

Status: code verified, 101 files readable, 11 matches

Tuesday, 16 June 2026 (1 paper)

[31] doi:10.1038/s41598-026-58107-8 [paper, data]

Three-dimensional voltage imaging in live larval zebrafish brains using fully genetically encoded voltage indicator.

Journal: Scientific reports

Status: data only, 1 dataset cited

Thursday, 11 June 2026 (1 paper)

[32] Code ↔ Paper doi:10.1016/j.isci.2026.116206 [paper, repository]

Gut distension evokes rapid neural dynamics in vagal and hindbrain populations of larval zebrafish.

Journal: iScience

Authors' code: gitlab.oit.duke.edu/ean26/arinel-et-al_2026 (no license), naumann-lab/caimageanalysis (no license), Naumann-Lab/alignment (MIT), Zenodo 20127931 (CC-BY-4.0), Zenodo 20128341 (MIT), arthur-pe/slicetca (MIT)

Status: code verified, 86 files readable, 19 matches

Tuesday, 9 June 2026 (1 paper)

[33] doi:10.1038/s41592-026-03125-7 [paper]

Simultaneous two- and three-photon multiplane imaging across cortical layers in freely moving mice.

Journal: Nature methods

Status: code on request

Monday, 8 June 2026 (1 paper)

[34] Code ↔ Paper doi:10.1016/j.crmeth.2026.101480 [paper, repository]

DeepFaceMouse enables scalable prediction of large-scale brain activity from facial dynamics in mice.

Journal: Cell reports methods

Authors' code: Zenodo 19644866 (CC-BY-4.0), yyildirimlab/DeepFaceMouse (MIT)

Status: code verified, 7 files readable, 5 matches

Friday, 5 June 2026 (1 paper)

[35] Code ↔ Paper doi:10.1016/j.crmeth.2026.101476 [paper, repository]

Unsupervised deep learning enables blur-free resolution enhancement in two-photon microscopy.

Journal: Cell reports methods

Authors' code: HaLU-9000/TENET (no license), Zenodo 19663648 (CC-BY-4.0)

Status: code verified, 47 files readable, 5 matches

Thursday, 4 June 2026 (1 paper)

[36] Code ↔ Paper doi:10.1016/j.celrep.2026.117456 [paper, repository]

Anterior lateral motor cortex enables contextual decision-making via dynamic reconfiguration of local circuits.

Journal: Cell reports

Authors' code: Zenodo 19828551 (CC-BY-4.0), asjessie/shadlen-lab (no license)

Status: code verified, 8 files readable, 2 matches

Monday, 1 June 2026 (3 papers)

[37] doi:10.1002/npr2.70113 [paper, data]

Transcranial Calcium Macro-Imaging From the Auditory Cortex of Thy1-Cre-Driven GCaMP8 Transgenic Rats.

Journal: Neuropsychopharmacology reports

Status: data only, 2 datasets cited

[38] Code ↔ Paper doi:10.1016/j.crmeth.2026.101472 [paper, repository]

Rapid neuronal labeling and functional imaging in the developing mouse brain with AAV-PHP.eB.

Journal: Cell reports methods

Authors' code: Zenodo 19838893 (CC-BY-4.0), cdeister/imageAnalysis_gui (MIT)

Status: code verified, 2,165 files readable

[39] Code ↔ Paper doi:10.1111/ejn.70582 [paper, repository]

Multifiber Array-Based Photometry System for Multiregional Functional Mapping in the Mouse Brain.

Journal: The European journal of neuroscience

Authors' code: Sakata-Lab/mfaCTpy (GPL-3.0), Sakata-Lab/MFA (GPL-3.0)

Status: code verified, 15 files readable

Friday, 29 May 2026 (1 paper)

[40] Code ↔ Paper doi:10.3389/fnsys.2026.1786396 [paper, repository]

Circuit dynamics of binocular conflict in mouse primary visual cortex.

Journal: Frontiers in systems neuroscience

Authors' code: danielmontgomery7/suppression-analysis-code (MIT)

Status: code verified, 127 files readable, 8 matches

Thursday, 28 May 2026 (1 paper)

[41] Code ↔ Paper doi:10.3389/fnsyn.2026.1832103 [paper, repository]

Automated ROI detection allows rapid quantification of synaptic activity across tens of thousands of synapses in cell culture.

Journal: Frontiers in synaptic neuroscience

Authors' code: jay-cee-begs/synaptic_suite2p (GPL-3.0)

Status: code verified, 24 files readable, 9 matches

Friday, 22 May 2026 (1 paper)

[42] Code ↔ Paper doi:10.1038/s41592-026-03066-1 [paper, repository]

A multimodal adaptive optical microscope for in vivo imaging from molecules to organisms.

Journal: Nature methods

Authors' code: scopetools/cudasirecon (GPL-3.0), abcucberkeley/PetaKit5D (GPL-3.0)

Status: code verified, 783 files readable, 4 matches

Wednesday, 20 May 2026 (2 papers)

[43] Code ↔ Paper doi:10.1016/j.xpro.2026.104591 [paper, repository]

Protocol for using the multi-cellular analysis toolbox in ImageJ for single-cell calcium imaging analysis.

Journal: STAR protocols

Authors' code: Zenodo 17610801 (MIT)

Status: code verified, 21 files readable, 1 match

[44] Code ↔ Paper doi:10.1038/s41467-026-73389-2 [paper, repository]

Physics-informed multi-encoder adaptive optics enables rapid aberration correction for intravital microscopy of deep complex tissue.

Journal: Nature communications

Authors' code: Zenodo 17118222 (CC-BY-4.0), lukachan41/MeNet-AO (MIT), Zenodo 19315205 (MIT)

Status: code verified, 52 files readable, 4 matches

Tuesday, 19 May 2026 (3 papers)

[45] Code ↔ Paper doi:10.1002/advs.202510822 [paper, repository]

How Neuromorphic Microstructures Control In Vitro Early-Stage Neuronal Outgrowth.

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Authors' code: CHARLESProtocol2/Neurite-Growth-Analysis-Toolkit (no license), EstherMatamoros/ProteinExpression (no license)

Status: code verified, 11 files readable, 3 matches

[46] Code ↔ Paper doi:10.1038/s41467-026-72710-3 [paper, repository]

A modular multi-color fluorescence microscope for simultaneous tracking of cellular activity and behavior.

Journal: Nature communications

Authors' code: scholz-lab.github.io/glowtracker (no license), scholz-lab/Macroscope-Paper (no license), scholz-lab/GlowTracker (GPL-3.0)

Status: code verified, 47 files readable, 6 matches

[47] doi:10.1038/s42003-026-10141-y [paper, data]

Directionally biased neuronal responses to pitch-axis vestibular stimulation in larval zebrafish compared to roll-axis responses.

Journal: Communications biology

Status: code on request, 1 dataset cited

Friday, 15 May 2026 (1 paper)

[48] doi:10.1016/j.xpro.2026.104564 [paper]

Protocol for monitoring neurotransmitter release upon projection-specific activation in mouse dorsal raphe nucleus via in vivo fiber photometry.

Journal: STAR protocols

Status: code on request

Wednesday, 13 May 2026 (1 paper)

[49] Code ↔ Paper doi:10.7554/elife.109888 [paper, repository]

Intravital calcium imaging of meningeal macrophages reveals niche-specific dynamics and aberrant responses to brain hyperexcitability.

Journal: eLife

Authors' code: levylabheadache/movieprocessing (GPL-3.0), levylabheadache/locomotion (GPL-3.0), levylabheadache/Aqua2Processing (GPL-3.0), levylabheadache/vasculature (no license), levylabheadache/GeneralLinearModel_Macrophages (GPL-3.0)

Status: code verified, 288 files readable, 20 matches

Tuesday, 12 May 2026 (1 paper)

[50] Code ↔ Paper doi:10.7554/elife.110277 [paper, repository]

Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals.

Journal: eLife

Authors' code: Neurocipher/PythonPipeline (no license), MetaCell/Zeiss-Data-Science (MIT)

Status: code verified, 27 files readable, 2 matches

Friday, 8 May 2026 (1 paper)

[51] Code ↔ Paper doi:10.3389/fnbeh.2026.1819512 [paper, repository]

iMOSS: an integrated open-source tail suspension test platform for high-resolution immobility scoring and synchronization with neural activity.

Journal: Frontiers in behavioral neuroscience

Authors' code: addy9908/iMOSS (MIT)

Status: code verified, 15 files readable, 7 matches

Wednesday, 6 May 2026 (1 paper)

[52] Code ↔ Paper doi:10.7554/elife.107518 [paper, repository]

Continuous flash suppression of neural responses and population orientation coding in macaque V1.

Journal: eLife

Authors' code: caviaryusi/CFS_2p (MIT)

Status: code verified, 16 files readable, 4 matches

Friday, 1 May 2026 (1 paper)

[53] Code ↔ Paper doi:10.1093/cercor/bhag062 [paper, repository]

Dynamic representations of valence in anterior cingulate cortex in mice.

Journal: Cerebral cortex (New York, N.Y. : 1991)

Authors' code: Zenodo 19339357 (CC-BY-4.0)

Status: code verified, 1 file readable, 2 matches

Friday, 17 April 2026 (2 papers)

[54] doi:10.1016/j.crmeth.2026.101412 [paper]

An improved preservation method for human dorsal root ganglion neurons enables wider access to human molecular pain neuroscience.

Journal: Cell reports methods

Status: code on request

[55] Code ↔ Paper doi:10.1016/j.molmet.2026.102372 [paper, repository]

AgRP neuron activity predicts and tracks the glycemic response to oral glucose.

Journal: Molecular metabolism

Authors' code: nikhayes/fibphoflow (MIT)

Status: code verified, 5 files readable

Wednesday, 15 April 2026 (2 papers)

[56] Code ↔ Paper doi:10.1002/advs.202519479 [paper, repository]

Diminished Signal-to-Noise Ratio Disrupts Somatosensory Population Encoding and Drives Tactile Hyposensitivity in the Fmr1<sup>-/y</sup> Autism Model.

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Authors' code: FrickLab/Imaging_2PCalciumAnalysis (GPL-2.0)

Status: code verified, 57 files readable, 14 matches

[57] Code ↔ Paper doi:10.1038/s41592-026-03043-8 [paper, repository]

Designer indicators for two-photon recording of subthreshold voltage dynamics.

Journal: Nature methods

Authors' code: reimerlab/jedi3-paper (no license)

Status: code verified, 11 files readable, 5 matches

Monday, 13 April 2026 (1 paper)

[58] doi:10.1038/s41377-026-02252-2 [paper, data]

Ultra-wide-field, deep, adaptive two-photon microscopy for multi-scale neuronal imaging.

Journal: Light, science & applications

Status: data only, 1 dataset cited

Friday, 10 April 2026 (1 paper)

[59] doi:10.1186/s11689-026-09692-2 [paper, data]

Altered folate metabolism disrupts auditory function from neonatal vocalizations to adult perceptual precision.

Journal: Journal of neurodevelopmental disorders

Status: data only, 2 datasets cited

Wednesday, 1 April 2026 (1 paper)

[60] Code ↔ Paper doi:10.1002/jbio.70260 [paper, repository]

Cell-MICS: Detecting Immune Cells With Label-Free Two-Photon Autofluorescence and Deep Learning.

Journal: Journal of biophotonics

Authors' code: lucaskreiss/multiphoton_imaging_with_computational_specificity (MIT)

Status: code verified, 16 files readable, 9 matches