optical imaging (calcium, voltage, 2-photon)

Modality: 605 papers with a page, 423 of them with their authors' code.

Sunday, 1 November 2026 (1 paper)

[1] Code ↔ Paper doi:10.1111/jne.70298 [paper, repository]

Arcuate kisspeptin neurons display two types of calcium events: Regulation by sex, gonads, and senktide.

Journal: Journal of neuroendocrinology

Authors' code: syncytium2/KNDy-Ca-1 (MIT), gibson-amandag/ArcKissCa_analysis (no license)

Status: code verified, 301 files readable, 5 matches

Thursday, 1 October 2026 (1 paper)

[2] Code ↔ Paper doi:10.1002/glia.70204 [paper, repository]

Müller Glia-Vasculature Interactions in the Developing Retina.

Journal: Glia

Authors' code: FellerLabCodeShare/Glia_Vasculature (no license)

Status: code verified, 4 files readable, 1 match

Monday, 28 September 2026 (1 paper)

[3] Code ↔ Paper doi:10.7554/elife.108236 [paper, repository]

Selective lifelong suppression of an odor processing channel in response to critical period experience.

Journal: eLife

Authors' code: adacks/Salman-et-al (no license)

Status: code verified, 1 file readable

Friday, 25 September 2026 (1 paper)

[4] 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)

[5] 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)

[6] 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)

[7] 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)

[8] 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

[9] 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

[10] 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)

[11] 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)

[12] 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)

[13] 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)

[14] 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)

[15] 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

[16] 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)

[17] 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)

[18] 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)

[19] 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)

[20] 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)

[21] 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)

[22] 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

[23] 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)

[24] 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)

[25] 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

[26] 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

[27] 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)

[28] 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)

[29] 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

[30] 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)

[31] 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, still to be checked

Thursday, 18 June 2026 (1 paper)

[32] 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)

[33] 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)

[34] 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)

[35] 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)

[36] 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)

[37] 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)

[38] 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)

[39] 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)

[40] 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

[41] 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

[42] 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)

[43] 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)

[44] 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)

[45] 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)

[46] 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

[47] 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)

[48] 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

[49] 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

[50] 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)

[51] 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)

[52] 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)

[53] 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)

[54] 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)

[55] 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)

[56] 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, 24 April 2026 (3 papers)

[57] Code ↔ Paper doi:10.1038/s41598-026-49531-x [paper, repository]

Population-scale analysis of frequency-dependent calcium dynamics in retinal ganglion cells under electric field stimulation.

Journal: Scientific reports

Authors' code: Omid-SH/RGCaEFS (MIT)

Status: code verified, 16 files readable, 5 matches

[58] Code ↔ Paper doi:10.1038/s41592-026-03065-2 [paper, repository]

PinkyCaMP: an mScarlet-based calcium sensor with enhanced brightness, photostability and multiplexing capabilities.

Journal: Nature methods

Authors' code: masseck/FibPho-PinkyCaMP (MIT)

Status: code verified, 4 files readable, 1 match

[59] Code ↔ Paper doi:10.1093/braincomms/fcag150 [paper, repository]

Using fibre photometry with a fluorescence resonance energy transfer-based biosensor to test efficacy of calpain inhibitors <i>in vivo</i>.

Journal: Brain communications

Authors' code: neurophotometrics (no license)

Status: code verified

Tuesday, 21 April 2026 (1 paper)

[60] doi:10.1016/j.molmet.2026.102371 [paper, data]

A distinct vagus-beta cell neural circuit senses glucose and modulates insulin secretion.

Journal: Molecular metabolism

Status: data only, 1 dataset cited

Friday, 17 April 2026 (2 papers)

[61] 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

[62] 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)

[63] 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

[64] 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)

[65] 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)

[66] 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)

[67] 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

Saturday, 28 March 2026 (1 paper)

[68] doi:10.1016/j.isci.2026.115514 [paper]

A dual-color miniature endoscope for calcium imaging in behaving mice.

Journal: iScience

Status: code on request

Thursday, 26 March 2026 (1 paper)

[69] doi:10.1073/pnas.2529147123 [paper, data]

Ultrasensitive measurement of brain penetration mechanics and blood vessel rupture with microscale probes.

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

Status: data only, 1 dataset cited

Wednesday, 25 March 2026 (2 papers)

[70] Code ↔ Paper doi:10.1088/1741-2552/ae4925 [paper, repository]

Computational optimization of two-photon holographic stimulation sites<i>in vivo</i>.

Journal: Journal of neural engineering

Authors' code: marcustriplett/photostim-optimizer (GPL-3.0)

Status: code verified, 9 files readable

[71] doi:10.1186/s12974-026-03771-w [paper, data]

Dynamics of neutrophilia at the neurovascular unit arising from repeated pulmonary inflammation.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

Tuesday, 24 March 2026 (1 paper)

[72] Code ↔ Paper doi:10.7554/elife.95525 [paper, repository]

A deep learning pipeline for mapping in situ network-level neurovascular coupling in multi-photon fluorescence microscopy.

Journal: eLife

Authors' code: AICONSlab/novas3d (GPL-3.0)

Status: code verified, 10 files readable, 5 matches

Monday, 23 March 2026 (1 paper)

[73] Code ↔ Paper doi:10.1016/j.xpro.2026.104443 [paper, repository]

Protocol for identifying and comparing neuronal ensembles using different algorithms within a graphical user interface.

Journal: STAR protocols

Authors' code: rivelco/ENCORE (GPL-3.0), hanshuting/SVDEnsemble (MIT), tortlab/Cell-Assembly-Detection (no license), brincolab/NeuralEnsembles (no license), GoodhillLab/neural-assembly-detection (GPL-3.0), PerezOrtegaJ/Xsembles2P (GPL-3.0)

Status: code verified, 643 files readable, 2 matches

Thursday, 19 March 2026 (1 paper)

[74] doi:10.1016/j.jneumeth.2026.110749 [paper, repository]

Evaluating linear model frameworks for directed predictive influence estimation from hypothalamic calcium imaging.

Journal: Journal of neuroscience methods

Authors' code: Zenodo 18102530 (GPL-3.0), oprisans/glm (GPL-3.0)

Status: code verified, 48 files readable, 7 matches

Wednesday, 18 March 2026 (1 paper)

[75] doi:10.7554/elife.106981 [paper, repository]

Formation of task representations and replay in mouse medial prefrontal cortex.

Journal: eLife

Authors' code: HamedShabani/PFC_sequence_analysis (no license), Zenodo 10528244 (CC-BY-4.0)

Status: code verified, 208 files readable, 4 matches

Monday, 16 March 2026 (1 paper)

[76] doi:10.1186/s43074-026-00237-3 [paper]

Needle beam two-photon microscopy for simultaneous multiplane neural and vascular imaging in awake mice.

Journal: PhotoniX

Status: code on request

Friday, 13 March 2026 (1 paper)

[77] doi:10.1523/eneuro.0459-25.2026 [paper, repository]

Open-Source Platform for Adjustable Training Regimes in Freely Moving and Head-Fixed Mice.

Journal: eNeuro

Authors' code: Mdcrespo/BehavioralPlatform (BSD-3-Clause)

Status: code verified, 21 files readable, 5 matches

Thursday, 12 March 2026 (1 paper)

[78] doi:10.1016/j.xpro.2026.104430 [paper, repository]

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

Journal: STAR protocols

Authors' code: tchetch12/IOI_Retinotopy_Analysis (no license), Zenodo 18662251 (CC-BY-4.0)

Status: code verified, 6 files readable

Wednesday, 11 March 2026 (1 paper)

[79] doi:10.64898/2026.03.09.710483 [paper, repository]

Multimodal reference brain atlas of adult <i>Danionella cerebrum</i>

Journal: bioRxiv (preprint)

Authors' code: gin.g-node.org/danionella/kadobianskyi_et_al_2026 (CC-BY-NC-SA-4.0)

Status: code verified, 4 files readable, 2 matches

Tuesday, 10 March 2026 (2 papers)

[80] doi:10.7554/elife.105081 [paper, repository]

Movie reconstruction from mouse visual cortex activity.

Journal: eLife

Authors' code: lRomul/sensorium (MIT), Joel-Bauer/movie_reconstruction_code (MIT)

Status: code verified, 44 files readable, 12 matches

[81] doi:10.1113/jp289290 [paper, repository]

Robust activity-dependent mitochondrial calcium dynamics at the AIS is dispensable for action potential generation.

Journal: The Journal of physiology

Authors' code: Kolelab/mtGCaMP (no license), microns-explorer.org (no license)

Status: code verified, 18 files readable

Monday, 9 March 2026 (2 papers)

[82] doi:10.1002/advs.202515887 [paper, repository]

An Open-Source Pipeline for Calcium Imaging and All-Optical Physiology in Human Stem Cell-Derived Neurons.

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

Authors' code: fdrgsp/micromanager-gui (BSD-3-Clause), fdrgsp/cali (BSD-3-Clause)

Status: code verified, 229 files readable, 19 matches

[83] doi:10.1371/journal.pone.0343516 [paper, data]

NeuronID: An automatic toolkit for identifying neurons in two-photon calcium imaging data.

Journal: PloS one

Status: data only, 1 dataset cited

Wednesday, 4 March 2026 (2 papers)

[84] doi:10.1038/s41467-026-69798-y [paper, repository]

Dual deconvolution in multiphoton structured illumination microscopy for deep-tissue super-resolution imaging.

Journal: Nature communications

Authors' code: CenterForDeepImaging/Dual-Deconvolution (no license), figshare 28600847 (CC-BY-4.0)

Status: code verified, 2 files readable, 1 match

[85] doi:10.1162/imag.a.1149 [paper]

An implanted lennula approach to measure neural Ca&lt;sup&gt;2+&lt;/sup&gt; responses in the awake marmoset visual cortex.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: code on request

Monday, 2 March 2026 (1 paper)

[86] doi:10.7554/elife.107939 [paper, repository]

Resolving synaptic events using subsynaptically targeted GCaMP8 variants.

Journal: eLife

Authors' code: linj7/CaFire (MIT), doi:10.5281/zenodo (no license), Zenodo 1552996 (CC0-1.0)

Status: code verified, 19 files readable, 1 match

Thursday, 26 February 2026 (1 paper)

[87] doi:10.1038/s41592-026-03006-z [paper, repository]

Next-generation multicolor indicators for in vivo imaging of norepinephrine.

Journal: Nature methods

Authors' code: PatriarchiLab/nLightG2 (GPL-3.0)

Status: code verified, 4 files readable, 3 matches

Tuesday, 24 February 2026 (1 paper)

[88] doi:10.1038/s41598-026-41049-6 [paper, repository]

Distinct neural signatures of hippocampal population dynamics during locomotion-in-place.

Journal: Scientific reports

Authors' code: samsoon-inayat/Toolbox (no license)

Status: dead link

Monday, 23 February 2026 (1 paper)

[89] doi:10.3389/fnsyn.2026.1741328 [paper, data]

Increased synaptic turnover in injured cortical axons: exploring the role of SARM1 ablation.

Journal: Frontiers in synaptic neuroscience

Status: data only, 1 dataset cited

Thursday, 19 February 2026 (1 paper)

[90] doi:10.1038/s41598-026-40218-x [paper, repository]

β-adrenergic receptors modulate CA1 population coding and synaptic plasticity during cumulative spatial memory formation and updating.

Journal: Scientific reports

Authors' code: johaubrich (no license)

Status: code verified

Wednesday, 18 February 2026 (1 paper)

[91] doi:10.1038/s41598-026-40269-0 [paper, repository]

LUMIN: an automated graphical analysis toolbox for high-throughput calcium imaging of in vitro neuronal cultures.

Journal: Scientific reports

Authors' code: kirkebylab/lumin](https: (no license)

Status: dead link

Monday, 16 February 2026 (1 paper)

[92] doi:10.1186/s12859-026-06385-4 [paper, repository]

Semi-automatic geometrical reconstruction and analysis of filopodia dynamics in 4D two-photon microscopy images.

Journal: BMC bioinformatics

Authors' code: zibamira/filopodia-tool (other)

Status: code verified, 160 files readable, 4 matches

Friday, 13 February 2026 (1 paper)

[93] doi:10.1016/j.crmeth.2026.101305 [paper, repository]

2P-FENDO-II: A fiber bundle microscope for all-optical, large field-of-view brain studies in freely moving mice.

Journal: Cell reports methods

Authors' code: photonics-VisionInstitute/2pFendo (MIT)

Status: empty repository, 2 files readable

Wednesday, 11 February 2026 (3 papers)

[94] doi:10.1007/s10571-026-01693-y [paper, data]

HDAC Inhibition Reshapes Splicing of Synaptic Plasticity-Related Genes and Neural Network Dynamics.

Journal: Cellular and molecular neurobiology

Status: data only, 1 dataset cited

[95] doi:10.1038/s41467-026-69419-8 [paper, repository]

Active pixel power control for crosstalk-free all-optical neural interrogation.

Journal: Nature communications

Authors' code: QuLab1234/APPC (no license)

Status: code verified, 4 files readable, 2 matches

[96] doi:10.1364/boe.579250 [paper]

Bessel beam side lobe suppression via non-degenerate two-photon excitation.

Journal: Biomedical optics express

Status: code on request

Monday, 9 February 2026 (1 paper)

[97] doi:10.1117/1.nph.13.s2.s23202 [paper, repository]

Voltage imaging as a window into neural computation.

Journal: Neurophotonics

Authors' code: Zenodo 6361012 (CC-BY-4.0), sihaziza/SpikeImagingAnalysis_public (no license)

Status: code verified, 486 files readable

Wednesday, 4 February 2026 (1 paper)

[98] doi:10.1016/j.crmeth.2025.101294 [paper, repository]

Neural barcoding representing cortical spatiotemporal dynamics based on continuous-time Markov chains.

Journal: Cell reports methods

Authors' code: Zenodo 17594529 (CC-BY-4.0), JMCulp/NeuralBarcode (CC-BY-4.0)

Status: code verified, 4 files readable

Sunday, 1 February 2026 (3 papers)

[99] doi:10.1117/1.nph.13.s2.s23203 [paper, repository]

MiniFAST: a sensitive and fast miniaturized microscope for &lt;i&gt;in vivo&lt;/i&gt; neural recording.

Journal: Neurophotonics

Authors' code: nelpy/nelpy (MIT)

Status: code verified, 97 files readable, 1 match

[100] doi:10.1117/1.nph.13.s2.s23206 [paper]

Combining membrane potential and calcium imaging in brain slices using the voltage-sensitive dye ElectroFluor630 and the calcium indicator Calbryte520.

Journal: Neurophotonics

Status: code on request

[101] doi:10.1117/1.nph.13.s2.s23207 [paper]

Multimodal optical imaging combining voltage-sensitive dye ElectroFluor630 with genetically encoded calcium, glutamate, or voltage indicators.

Journal: Neurophotonics

Status: code on request

Thursday, 29 January 2026 (3 papers)

[102] doi:10.1016/j.crmeth.2025.101298 [paper, repository]

A multicellular analysis calcium imaging toolbox for ImageJ.

Journal: Cell reports methods

Authors' code: JohnHageter/Multi-Cell-Analysis (MIT), Zenodo 17610802 (MIT)

Status: code verified, 42 files readable, 6 matches

[103] doi:10.1117/1.nph.13.1.015008 [paper]

Tonotopic organization in the basal region of the ventromedial nucleus of the thalamus revealed by fiber photometry recording.

Journal: Neurophotonics

Status: code on request

[104] doi:10.1364/boe.564339 [paper, repository]

Thermal lensing effects in two-photon light-sheet microscopy.

Journal: Biomedical optics express

Authors' code: LJPZebra/ThermalLens (no license)

Status: code verified, 14 files readable, 4 matches

Tuesday, 27 January 2026 (2 papers)

[105] doi:10.1523/eneuro.0378-25.2025 [paper, repository]

Reliable Inference of the Encoding of Task States by Individual Neurons Using Calcium Imaging.

Journal: eNeuro

Authors' code: Zenodo 15708398 (CC-BY-4.0)

Status: code verified

[106] doi:10.7554/elife.98122 [paper, repository]

Synaptic mechanisms modulate the spatiotemporal dynamics of striatal direct pathway neurons and motor output.

Journal: eLife

Authors' code: JMarshall-8413/Marshall_2025_SourceCode (GPL-3.0)

Status: code verified, 21 files readable, 7 matches

Saturday, 24 January 2026 (1 paper)

[107] doi:10.1117/1.nph.13.1.015007 [paper, repository]

Desensitization of opsin responses during all-optical interrogation depends on imaging parameters.

Journal: Neurophotonics

Authors' code: BlakeRussell98/C1V1_desensitization (no license)

Status: code verified, 28 files readable

Tuesday, 20 January 2026 (1 paper)

[108] doi:10.1117/1.nph.13.1.015004 [paper, repository]

Cellular multipoint adaptive technology for two-photon mesoscope.

Journal: Neurophotonics

Authors' code: cssyyyjl/CMAT-PAPER_DATA (no license)

Status: code verified

Sunday, 18 January 2026 (1 paper)

[109] doi:10.64898/2026.01.16.699885 [paper, repository]

Hippocampal neuronal and astrocytic responses to noradrenaline and natural arousal

Journal: bioRxiv (preprint)

Authors' code: PTRRupprecht/Drawing-ROIs-without-GUI (MIT), PTRRupprecht/Duss-et-al-2026 (GPL-3.0)

Status: code verified, 24 files readable

Tuesday, 6 January 2026 (1 paper)

[110] doi:10.1117/1.nph.13.1.015002 [paper]

Diurnal differences in cerebral microvascular blood flow and oxygen delivery across brain regions in awake mice.

Journal: Neurophotonics

Status: code on request

Friday, 2 January 2026 (1 paper)

[111] doi:10.1117/1.jbo.31.1.016004 [paper, repository]

Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer's disease.

Journal: Journal of biomedical optics

Authors' code: estassss/Longitudinal-three-photon-imaging (no license)

Status: code verified, 15 files readable, 6 matches

Thursday, 1 January 2026 (5 papers)

[112] doi:10.1002/cpz1.70286 [paper, repository]

A Protocol for Microprism-Based Two-Photon Imaging Of The Lateral Cortex In The Mouse Inferior Colliculus.

Journal: Current protocols

Authors' code: Zenodo 14946966 (MIT)

Status: code verified, 47 files readable, 1 match

[113] doi:10.1002/dneu.70007 [paper, repository]

Parallel Morphological and Functional Development in the Xenopus Retinotectal System.

Journal: Developmental neurobiology

Authors' code: figshare 267521 (CC-BY-4.0), RuthazerLab/XenMorphFunc (no license)

Status: code verified, 7 files readable, 4 matches

[114] doi:10.1117/1.nph.13.1.015010 [paper, repository]

Mapping functional connectivity in the pigeon brain with wide-field optical imaging.

Journal: Neurophotonics

Authors' code: mehdibehroozi/sleeping_pigeon_fMRI (no license), brierl/Mouse_WOI (no license)

Status: code verified, 169 files readable, 6 matches

[115] doi:10.1117/1.nph.13.1.015013 [paper, repository]

Open-source modular field-programmable gate array system for two-photon mesoscope enabling multiarea, multidepth neural activity recording and lifetime imaging.

Journal: Neurophotonics

Authors' code: dropbox.com/scl/fo (no license)

Status: code verified

[116] doi:10.1117/1.nph.13.1.015014 [paper, repository]

Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise.

Journal: Neurophotonics

Authors' code: WUSTL-CulverLab/Thermal-Two-Photon-Imaging-Code (no license)

Status: code verified, 40 files readable, 5 matches

Wednesday, 31 December 2025 (1 paper)

[117] doi:10.59390/001c.154223 [paper, repository]

An Advanced Undergraduate Laboratory Course: Calcium Imaging and Data Analysis - a Mini Graduate Research Experience.

Journal: Journal of undergraduate neuroscience education : JUNE : a publication of FUN, Faculty for Undergraduate Neuroscience

Authors' code: hbai521/calcium_imaging (no license)

Status: code verified, 9 files readable, 3 matches

Thursday, 25 December 2025 (1 paper)

[118] doi:10.64898/2025.12.23.696162 [paper, repository]

Multi-fiber array-based photometry system for multi-regional functional mapping in the mouse brain

Journal: bioRxiv (preprint)

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

Status: code verified, 15 files readable

Thursday, 18 December 2025 (1 paper)

[119] doi:10.1016/j.isci.2025.114487 [paper]

Environmental enrichment accelerates the stabilization of cortical representation during &lt;i&gt;de novo&lt;/i&gt; learning.

Journal: iScience

Status: code on request

Monday, 15 December 2025 (1 paper)

[120] doi:10.1038/s42003-025-09357-1 [paper, repository]

Low-dimensional signatures of neuronal activity associated with long-term operant conditioning in Aplysia.

Journal: Communications biology

Authors' code: Byrne-Lab/VSD_CFE_analysis (no license), OSF qb59g (no license), Byrne-Lab/Vanaki (no license)

Status: code verified, 62 files readable, 4 matches

Friday, 12 December 2025 (1 paper)

[121] doi:10.1093/biomethods/bpaf090 [paper, repository]

The protocol for mesoscopic wide-field optical imaging in mice: from zero to hero.

Journal: Biology methods & protocols

Authors' code: natalia1896/WIFIOPIA (no license)

Status: code verified, 18 files readable, 8 matches

Thursday, 11 December 2025 (1 paper)

[122] doi:10.1016/j.celrep.2025.116682 [paper, repository]

The relevance of context in memory tasks influences the magnitude of hippocampal remapping.

Journal: Cell reports

Authors' code: Zenodo 17488388 (CC-BY-4.0), ewellneurolab/discrimination-ca1 (no license)

Status: code verified, 230 files readable, 14 matches

Wednesday, 10 December 2025 (2 papers)

[123] doi:10.7554/elife.107540 [paper, repository]

Longitudinal tracking of neuronal activity from the same cells in the developing brain using Track2p.

Journal: eLife

Authors' code: track2p.github.io/home.html (no license), juremaj/track2p (GPL-3.0), basler/pypylon (BSD-3-Clause), track2p.github.io/run_inputs_and_parameters (no license)

Status: code verified, 263 files readable, 3 matches

[124] doi:10.3389/fphys.2025.1708686 [paper, data]

Tmem45b modulates itch via endoplasmic reticulum calcium regulation.

Journal: Frontiers in physiology

Status: data only, 1 dataset cited

Tuesday, 9 December 2025 (1 paper)

[125] doi:10.1038/s41592-025-02925-7 [paper, repository]

FACED 2.0 enables large-scale voltage and calcium imaging in vivo.

Journal: Nature methods

Authors' code: JiLabUCBerkeley/FACED2PFM2p0-analysis (GPL-3.0)

Status: empty repository, 2 files readable

Tuesday, 2 December 2025 (3 papers)

[126] doi:10.1038/s41592-025-02972-0 [paper, repository]

CaBLAM: a high-contrast bioluminescent Ca&lt;sup&gt;2+&lt;/sup&gt; indicator derived from an engineered Oplophorus gracilirostris luciferase.

Journal: Nature methods

Authors' code: NICALab/SUPPORT (GPL-3.0), Shaner-Lab/CaBLAM (CC0-1.0)

Status: code verified, 46 files readable, 18 matches

[127] doi:10.1038/s42003-025-09122-4 [paper, repository]

Multi-modal label-free imaging of cellular metabolism and oxidative stress in 3D brain tissue models.

Journal: Communications biology

Authors' code: Zenodo 17228894 (CC-BY-4.0)

Status: code verified, 14 files readable

[128] doi:10.1364/boe.576516 [paper, data]

Miniaturized widefield microscope for high speed in vivo voltage imaging.

Journal: Biomedical optics express

Status: data only, 1 dataset cited

Saturday, 29 November 2025 (1 paper)

[129] doi:10.1038/s41467-025-66922-2 [paper, repository]

High-throughput two-photon volumetric brain imaging in freely moving mice.

Journal: Nature communications

Authors' code: WuLab-CIBR/miniBB2p (MIT), Zenodo 17423404 (MIT)

Status: code verified, 4 files readable

Tuesday, 25 November 2025 (2 papers)

[130] doi:10.1073/pnas.2510337122 [paper, repository]

Light-field deep learning enables high-throughput, scattering-mitigated calcium imaging.

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

Authors' code: afoust/LNet_jGCaMP8f_pipelines (MIT), Zenodo 14900716 (CC-BY-NC-ND-4.0)

Status: code verified, 13 files readable, 4 matches

[131] doi:10.1016/j.jbc.2025.110975 [paper, data]

Development of a VHH that inhibits the binding of neuronal pentraxin 2 to a postsynaptic glutamate receptor, AMPAR.

Journal: The Journal of biological chemistry

Status: data only, 1 dataset cited

Wednesday, 19 November 2025 (1 paper)

[132] doi:10.1016/j.isci.2025.114141 [paper, repository]

Deep learning-enabled high-performance multiphoton fluorescence vascular imaging using clinically approved fluorescent probes.

Journal: iScience

Authors' code: lhr314/MPFI_vessels_denoising (no license)

Status: code verified, 26 files readable, 5 matches

Tuesday, 18 November 2025 (1 paper)

[133] doi:10.1002/advs.202509707 [paper, data]

The Geometry of Layer 2/3 Cortical Sound Processing in Slow Wave Sleep.

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

Status: data only, 1 dataset cited

Wednesday, 12 November 2025 (1 paper)

[134] doi:10.1016/j.ohx.2025.e00721 [paper, repository]

A device for simultaneous neural recording and drug infusion in rodents.

Journal: HardwareX

Authors' code: Zenodo 17435776 (CC-BY-4.0)

Status: code verified, 1 file readable

Monday, 10 November 2025 (1 paper)

[135] doi:10.1016/j.crmeth.2025.101221 [paper, data]

High-speed neural imaging with multiplexed miniaturized two-photon microscopy.

Journal: Cell reports methods

Status: code on request, 1 dataset cited

Monday, 3 November 2025 (1 paper)

[136] doi:10.1016/j.crmeth.2025.101216 [paper, repository]

Combinatorial responsiveness of chemosensory neurons in mouse explants revealed by DynamicNeuroTracker.

Journal: Cell reports methods

Authors' code: JungsikNoh/DynamicNeuronTracker (GPL-3.0), Zenodo 17114104 (GPL-3.0), DanuserLab/u-track3D (GPL-3.0)

Status: code verified, 2,045 files readable, 17 matches

Saturday, 1 November 2025 (1 paper)

[137] doi:10.1111/ejn.70268 [paper, repository]

Ex Vivo Modulation of the BNST by Parabrachial CGRP Projections Is Decreased After a History of Stress-Induced Anxiety.

Journal: The European journal of neuroscience

Authors' code: zhoupc/CNMF_E (GPL-3.0)

Status: code verified, 266 files readable, 2 matches

Thursday, 30 October 2025 (2 papers)

[138] doi:10.3389/fninf.2025.1700481 [paper, repository]

Information-theoretic gradient flows in mouse visual cortex.

Journal: Frontiers in neuroinformatics

Authors' code: allavailablepubliccode/info_flow (no license)

Status: code verified, 11 files readable, 8 matches

[139] doi:10.1016/j.isci.2025.113898 [paper, repository]

Rapid neonatal AAV delivery for adult cortical two-photon imaging of genetically encoded sensors.

Journal: iScience

Authors' code: mjskay/ARTool (GPL), Zenodo 17117568 (GPL-2.0), proektlab/wisser_blackwood_fig8_2p_analysis (GPL-2.0)

Status: code verified, 275 files readable, 7 matches

Monday, 27 October 2025 (1 paper)

[140] doi:10.7554/elife.99989 [paper, repository]

Tonotopy is not preserved in a descending stage of auditory cortex.

Journal: eLife

Authors' code: xieyangshuying/Tonotopy (Apache-2.0)

Status: code verified, 10 files readable

Thursday, 23 October 2025 (1 paper)

[141] doi:10.1038/s41467-025-64431-w [paper, repository]

Correlative voltage imaging and cryo-electron tomography bridge neuronal activity and molecular structure.

Journal: Nature communications

Authors' code: Dangallll/CoVET (no license)

Status: code verified, 3 files readable

Wednesday, 22 October 2025 (1 paper)

[142] doi:10.1117/1.nph.12.4.045004 [paper]

Real-time single-vessel analysis reveals vascular-type-dependent blood-brain barrier dysfunction in rodent models of status epilepticus and neuroinflammation.

Journal: Neurophotonics

Status: code on request

Tuesday, 21 October 2025 (1 paper)

[143] doi:10.1073/pnas.2503576122 [paper, repository]

Descattering and image restoration with a transformer-based neural network in deep tissue imaging.

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

Authors' code: Xu-onion/DA-net (no license)

Status: code verified, 8 files readable, 3 matches

Thursday, 16 October 2025 (1 paper)

[144] doi:10.1016/j.celrep.2025.116443 [paper]

Modulation of speed-dependent acetylcholine release in the hippocampus by spatial task engagement.

Journal: Cell reports

Status: code on request

Wednesday, 15 October 2025 (2 papers)

[145] doi:10.1038/s41467-025-64251-y [paper, repository]

Rapid adaptive optics enabling near noninvasive high-resolution brain imaging in awake behaving mice.

Journal: Nature communications

Authors' code: QuLab1234/MD-FSS (no license)

Status: code verified, 1 file readable

[146] doi:10.1016/j.celrep.2025.116383 [paper, repository]

Hippocampal sequences represent working memory and implicit timing.

Journal: Cell reports

Authors' code: ccdorian/dDNMS2025 (no license)

Status: code verified, 19 files readable, 6 matches

Wednesday, 8 October 2025 (2 papers)

[147] doi:10.1523/jneurosci.0133-25.2025 [paper, repository]

Cholinergic Dynamics in the Septo-hippocampal System Provide Phasic Multiplexed Signals for Spatial Novelty and Correlate with Behavioral States.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Authors' code: dannenberglab/Cholinergic-dynamics-in-spatial-exploration (no license)

Status: code verified, 6 files readable, 4 matches

[148] doi:10.1073/pnas.2426241122 [paper, data]

Transpupillary in vivo two-photon imaging reveals enhanced surveillance of retinal microglia in diabetic mice.

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

Status: data only, 1 dataset cited

Thursday, 2 October 2025 (1 paper)

[149] doi:10.1371/journal.pbio.3003376 [paper, repository]

Cortical astrocyte histamine-1-receptors regulate intracellular calcium and extracellular adenosine dynamics across sleep and wake.

Journal: PLoS biology

Authors' code: Zenodo 16809849 (CC-BY-4.0)

Status: code verified, 7 files readable, 26 matches

Tuesday, 30 September 2025 (1 paper)

[150] doi:10.7554/elife.103676 [paper, repository]

Diverse calcium dynamics underlie place field formation in hippocampal CA1 pyramidal cells.

Journal: eLife

Authors' code: hdl.handle.net/21.15109/arp (no license)

Status: code verified

Thursday, 18 September 2025 (3 papers)

[151] doi:10.1016/j.celrep.2025.116294 [paper]

Circuit-selective pharmacological targeting of prefrontal cortex-projecting locus coeruleus neurons drives antinociception.

Journal: Cell reports

Status: code on request

[152] doi:10.1016/j.crmeth.2025.101180 [paper, repository]

A real-time all-optical interface for dynamic perturbation of neural activity during behavior.

Journal: Cell reports methods

Authors' code: Zenodo 16424873 (CC-BY-4.0), alloptical/pyRTAOI (GPL-2.0)

Status: code verified, 322 files readable, 12 matches

[153] doi:10.1016/j.crmeth.2025.101179 [paper, repository]

A deep learning pipeline for accurate and automated restoration, segmentation, and quantification of dendritic spines.

Journal: Cell reports methods

Authors' code: Zenodo 15612240 (GPL-3.0), lahammond/RESPAN (GPL-3.0), Zenodo 19671935 (CC-BY-NC-4.0), Zenodo 19671936 (CC-BY-NC-4.0), Zenodo 19672042 (CC-BY-NC-4.0), Zenodo 19672043 (CC-BY-NC-4.0), Zenodo 19671964 (CC-BY-NC-4.0), Zenodo 19671965 (CC-BY-NC-4.0), Zenodo 19671948 (CC-BY-NC-4.0), Zenodo 19671949 (CC-BY-NC-4.0)

Status: code verified, 52 files readable, 4 matches

Wednesday, 17 September 2025 (1 paper)

[154] doi:10.1038/s41593-025-02024-y [paper, repository]

High-throughput synaptic connectivity mapping using in vivo two-photon holographic optogenetics and compressive sensing.

Journal: Nature neuroscience

Authors' code: photonics-VisionInstitute/CS-connectivity (no license), Oweiss-Lab/Compressed-Sensing-Connectivity-Mapping (MIT)

Status: code verified, 12 files readable, 1 match

Tuesday, 16 September 2025 (1 paper)

[155] doi:10.1016/j.celrep.2025.116291 [paper]

Clearing truncated tau protein restores neuronal function and prevents microglia activation in tauopathy mice.

Journal: Cell reports

Status: code on request

Friday, 12 September 2025 (1 paper)

[156] doi:10.1126/sciadv.adr6687 [paper, repository]

DeepInMiniscope: Deep learning-powered physics-informed integrated miniscope.

Journal: Science advances

Authors' code: doi:10.5061/dryad.6t1g1jx83 (no license), Yang-Research-Laboratory/DeepInMiniscope-Learned-Integrated-Miniscope (MIT), Zenodo 14172156 (MIT)

Status: code verified, 15 files readable, 1 match

Thursday, 11 September 2025 (1 paper)

[157] doi:10.1016/j.brs.2025.09.004 [paper, repository]

Transcranial ultrasound stimulation modulates neuronal membrane potentials across broad timescales in the awake mammalian brain.

Journal: Brain stimulation

Authors' code: HanLabBU/TUS-Brain-Stimulation-2025 (no license)

Status: code verified, 7 files readable, 7 matches

Sunday, 7 September 2025 (2 papers)

[158] doi:10.1016/j.xpro.2025.104068 [paper]

Protocol for live-cell calcium imaging of human lung microvascular endothelial vessel-on-a-chip model.

Journal: STAR protocols

Status: code on request

[159] doi:10.1016/j.isci.2025.113525 [paper, repository]

An extension module for a two-photon microscope enables flexible &lt;i&gt;in vivo&lt;/i&gt; imaging and all-optical physiology.

Journal: iScience

Authors' code: rysk-t/ex2p (MIT), Zenodo 15392791 (MIT)

Status: code verified, 4 files readable

Friday, 5 September 2025 (1 paper)

[160] doi:10.1016/j.celrep.2025.116219 [paper]

Adverse gestational environment configures a subpopulation of ventral dentate granule cells for recruitment to drive innate anxiety.

Journal: Cell reports

Status: code on request

Wednesday, 3 September 2025 (2 papers)

[161] doi:10.1523/jneurosci.0102-25.2025 [paper, repository]

Optical Recordings of Unitary Synaptic Connections Reveal High and Random Local Connectivity between CA3 Pyramidal Cells.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Authors' code: repo.researchdata.hu/dataverse/szabadics_lab (no license)

Status: code verified

[162] doi:10.1371/journal.pbio.3003359 [paper, repository]

Short-term memory errors are strongly associated with a drift in neural activity in the posterior parietal cortex.

Journal: PLoS biology

Authors' code: Zenodo 15872574 (CC-BY-4.0)

Status: code verified

Monday, 1 September 2025 (1 paper)

[163] doi:10.1167/iovs.66.12.25 [paper, repository]

Inner Limiting Membrane Peel Extends In Vivo Calcium Imaging of Retinal Ganglion Cell Activity Beyond the Fovea in Non-Human Primate.

Journal: Investigative ophthalmology & visual science

Authors' code: OSF dwck8 (no license)

Status: code verified, 35 files readable, 5 matches

Friday, 29 August 2025 (1 paper)

[164] doi:10.1016/j.nbd.2025.107072 [paper, repository]

Spontaneous pathology in PS19 tauopathy mice progresses via brain networks.

Journal: Neurobiology of disease

Authors' code: Zenodo 7942188 (no license)

Status: empty repository

Thursday, 28 August 2025 (1 paper)

[165] doi:10.1073/pnas.2515113122 [paper, repository]

Amyloid β-dependent neuronal silencing through synaptic decoupling.

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

Authors' code: Zenodo 16837260 (CC-BY-4.0)

Status: code verified

Tuesday, 26 August 2025 (2 papers)

[166] doi:10.1073/pnas.2504264122 [paper, data]

Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice.

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

Status: data only, 1 dataset cited

[167] doi:10.1186/s12859-025-06206-0 [paper, repository]

Calciumnetexplorer: an R package for network analysis of calcium imaging data.

Journal: BMC bioinformatics

Authors' code: simo-91/CalNetExploreR (other)

Status: code verified, 24 files readable, 9 matches

Saturday, 23 August 2025 (1 paper)

[168] doi:10.1016/j.celrep.2025.116187 [paper, repository]

Striatal output regulates the postnatal maturation of cortical circuits.

Journal: Cell reports

Authors' code: Zenodo 15791388 (CC-BY-4.0), LarsHenrikNelson/ClampSuite (GPL-3.0), peixoto-lab/janecek_2025 (no license)

Status: code verified, 51 files readable, 4 matches

Wednesday, 20 August 2025 (1 paper)

[169] doi:10.3389/fnagi.2025.1550673 [paper, repository]

Disrupted calcium dynamics and electrophysiological activity in the stratum pyramidale and hippocampal alveus during fear conditioning in the 5xFAD model of Alzheimer's disease.

Journal: Frontiers in aging neuroscience

Authors' code: lmn-projects/wes-2.0 (no license), bothlab/pomidaq (LGPL-3.0), syntalos/syntalos (no license), AutoHotkey/AutoHotkey (GPL-2.0), denisecailab/minian (GPL-3.0), spbstu-applied-math/NeuroActivityToolkit (no license)

Status: code verified, 1,054 files readable, 3 matches

Friday, 15 August 2025 (1 paper)

[170] doi:10.1101/2025.08.12.669914 [paper, repository]

Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer’s disease

Journal: bioRxiv (preprint)

Authors' code: estassss/Longitudinal-three-photon-imaging (no license)

Status: code verified, 15 files readable

Thursday, 14 August 2025 (2 papers)

[171] doi:10.1523/eneuro.0221-25.2025 [paper, repository]

FiPhoPHA-A Fiber Photometry Python Package for Post Hoc Analysis.

Journal: eNeuro

Authors' code: philjrdb/FibPhotom (no license), VasiliDrakopoulos/fiphopha (MIT)

Status: code verified, 28 files readable, 2 matches

[172] doi:10.1073/pnas.2503139122 [paper, repository]

Layer 1 NDNF interneurons form distinct subpopulations with opposite activation patterns during sleep in freely behaving mice.

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

Authors' code: AurelieBre/L1NDNFsubpop_PNAS2025 (no license), denisecailab/minian (GPL-3.0)

Status: code verified, 76 files readable, 7 matches

Wednesday, 13 August 2025 (2 papers)

[173] doi:10.1016/j.xpro.2025.104030 [paper, repository]

Protocol for detecting neuronal subnetworks from in vivo calcium imaging data using multiple clustering algorithms in MATLAB.

Journal: STAR protocols

Authors' code: EdnaHuang/Subnetwork-clustering-lme-modeling (Apache-2.0), cossartlab/code-modol-et-al.-2020 (no license), Zenodo 15856749 (Apache-2.0)

Status: code verified, 183 files readable, 40 matches

[174] doi:10.3389/fncom.2025.1639829 [paper, data]

Maximum likelihood estimation of spatially dependent interactions in large populations of cortical neurons.

Journal: Frontiers in computational neuroscience

Status: data only, 1 dataset cited

Tuesday, 12 August 2025 (2 papers)

[175] doi:10.1186/s13578-025-01458-y [paper, repository]

Lysophosphatidic acid selectively modulates excitatory transmission in hippocampal neurons.

Journal: Cell & bioscience

Authors' code: konstantinstadler/brandt_lpa_neuronal_modulation (MIT)

Status: code verified, 4 files readable

[176] doi:10.1016/j.celrep.2025.116148 [paper]

High-speed voltage imaging of action potentials in molecular layer interneurons reveals sensory-driven synchrony that augments movement.

Journal: Cell reports

Status: code on request

Monday, 11 August 2025 (1 paper)

[177] doi:10.1016/j.cell.2025.07.024 [paper, data]

Molecular and neural control of social hierarchy by a forebrain-thalamocortical circuit.

Journal: Cell

Status: data only, 1 dataset cited

Friday, 8 August 2025 (1 paper)

[178] doi:10.1126/sciadv.ads1807 [paper, data]

Positive-going hybrid indicators for voltage imaging in excitable cells and tissues.

Journal: Science advances

Status: data only, 1 dataset cited

Thursday, 7 August 2025 (3 papers)

[179] doi:10.1002/ame2.70073 [paper, data]

Insight into pericytes in glioblastoma angiogenesis: In vivo tracking by two-photon microscopy and proteomic profiling.

Journal: Animal models and experimental medicine

Status: data only, 1 dataset cited

[180] doi:10.1038/s41377-025-01895-x [paper, repository]

Multi-photon, label-free photoacoustic and optical imaging of NADH in brain cells.

Journal: Light, science & applications

Authors' code: surlab/lf-mp-photoacoustic-imaging (MIT)

Status: code verified, 234 files readable, 1 match

[181] doi:10.1111/acer.70132 [paper, repository]

A model of ethanol self-administration in head-fixed mice.

Journal: Alcohol, clinical & experimental research

Authors' code: Otis-Lab-MUSC/REACHER (Unlicense)

Status: code verified, 145 files readable

Wednesday, 6 August 2025 (1 paper)

[182] doi:10.1523/jneurosci.2405-24.2025 [paper]

Nicotine Withdrawal Drives Aversive Behaviors by Recruiting Inhibitory Interpeduncular Nucleus Inputs to the Laterodorsal Tegmentum in Mice.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Status: code on request

Monday, 4 August 2025 (1 paper)

[183] doi:10.7554/elife.101440 [paper, repository]

Odors drive feeding through gustatory receptor neurons in &lt;i&gt;Drosophila&lt;/i&gt;.

Journal: eLife

Authors' code: hpwei82/2022_hpwei (MIT)

Status: code verified, 19 files readable, 5 matches

Sunday, 3 August 2025 (1 paper)

[184] doi:10.1038/s41467-025-62534-y [paper, repository]

Open-source, high performance miniature 2-photon microscopy systems for freely behaving animals.

Journal: Nature communications

Authors' code: golshanilab/UCLA_2P_Miniscope (GPL-3.0)

Status: code verified, 4 files readable, 3 matches

Friday, 1 August 2025 (1 paper)

[185] doi:10.1093/cercor/bhaf203 [paper, repository]

Activity of CaMKII-expressing neurons in medial prefrontal cortex of male and female Long-Evans rats is necessary for encoding odor information and novelty recognition in an odor-based incidental memory test.

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

Authors' code: dterstege/publicationrepo (no license)

Status: code verified, 15 files readable, 4 matches

Wednesday, 30 July 2025 (1 paper)

[186] doi:10.1016/j.crmeth.2025.101116 [paper]

AAV vectors for specific and efficient gene expression in microglia.

Journal: Cell reports methods

Status: code on request

Tuesday, 29 July 2025 (3 papers)

[187] doi:10.1038/s41597-025-05482-y [paper, repository]

Multimodal dataset linking wide-field calcium imaging to behavior changes in operant lever-pull task in mice.

Journal: Scientific data

Authors' code: BraiDyn-BC/bdbc-data-pipeline (MIT)

Status: code verified, 4 files readable, 1 match

[188] doi:10.1016/j.xpro.2025.103996 [paper]

Protocol to study adenosine release in the adult mouse hippocampus using a genetically encoded sensor, 2-photon live imaging, and fiber photometry.

Journal: STAR protocols

Status: code on request

[189] doi:10.3389/fnins.2025.1620654 [paper, repository]

Contribution of individual excitatory synapses on dendritic spines to electrical signaling.

Journal: Frontiers in neuroscience

Authors' code: modeldb:2016666 (no license)

Status: code verified

Friday, 25 July 2025 (1 paper)

[190] doi:10.3390/ijms26157180 [paper, repository]

AI-Powered Mice Behavior Tracking and Its Application for Neuronal Manifold Analysis Based on Hippocampal Ensemble Activity in an Alzheimer's Disease Mice Model.

Journal: International journal of molecular sciences

Authors' code: Biomed-imaging-lab/AI-mouse-detector (no license)

Status: code verified, 10 files readable, 2 matches

Tuesday, 22 July 2025 (3 papers)

[191] doi:10.1038/s41593-025-02016-y [paper, repository]

Voltage imaging reveals hippocampal inhibitory dynamics shaping pyramidal memory-encoding sequences.

Journal: Nature neuroscience

Authors' code: jtaxidis-sickkids/Taxidis-et-al.-2025 (MIT)

Status: code verified, 167 files readable, 27 matches

[192] doi:10.1016/j.xpro.2025.103972 [paper, repository]

Protocol for recording neuronal activity in food and cocaine self-administration in freely behaving mice using calcium imaging.

Journal: STAR protocols

Authors' code: liang-bo/AutoStereota (MIT), schnitzer-lab/EXTRACT-public (MIT)

Status: code verified, 188 files readable

[193] doi:10.1016/j.celrep.2025.116037 [paper, repository]

RNA-programmable cell-type monitoring and manipulation in the human cortex with CellREADR.

Journal: Cell reports

Authors' code: AllenInstitute/scrattch.hicat (BSD-2-Clause)

Status: code verified, 66 files readable, 4 matches

Friday, 18 July 2025 (1 paper)

[194] doi:10.3390/cells14141103 [paper]

IP3R2-Mediated Astrocytic Ca&lt;sup&gt;2+&lt;/sup&gt; Transients Are Critical to Sustain Modulatory Effects of Locomotion on Neurons in Mouse Somatosensory Cortex.

Journal: Cells

Status: code on request

Wednesday, 16 July 2025 (1 paper)

[195] doi:10.1016/j.cell.2025.06.028 [paper, repository]

Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals.

Journal: Cell

Authors' code: schnitzer-lab/CoReU (no license), Zenodo 15686223 (CC-BY-4.0), sihaziza/uSMAART_public (GPL-3.0), Zenodo 15679319 (CC-BY-4.0), schnitzer-lab/TEMPO-processing (no license)

Status: code verified, 276 files readable, 9 matches

Tuesday, 15 July 2025 (2 papers)

[196] doi:10.1523/eneuro.0009-25.2025 [paper, repository]

CalTrig: A GUI-Based Machine Learning Approach for Decoding Neuronal Calcium Transients in Freely Moving Rodents.

Journal: eNeuro

Authors' code: cci-malab/calcium-transient-analysis (GPL-3.0)

Status: code verified, 40 files readable, 15 matches

[197] doi:10.1038/s41597-025-05527-2 [paper, repository]

24-hour simultaneous mPFC's miniature 2-photon imaging, EEG-EMG, and video recording during natural behaviors.

Journal: Scientific data

Authors' code: doi:10.12751/g-node.1762hn (no license)

Status: code verified

Monday, 14 July 2025 (2 papers)

[198] doi:10.1038/s41467-025-61532-4 [paper, repository]

Deep-tissue high-sensitivity multimodal imaging and optogenetic manipulation enabled by biliverdin reductase knockout.

Journal: Nature communications

Authors' code: gitlab.oit.duke.edu/pilab/blvra (no license)

Status: code verified, 3 files readable

[199] doi:10.1016/j.celrep.2025.115991 [paper]

Physiological and injury-induced microglial dynamics across the lifespan.

Journal: Cell reports

Status: code on request

Saturday, 5 July 2025 (1 paper)

[200] doi:10.21769/bioprotoc.5371 [paper, repository]

Two-photon (2P) Microscopy to Study Ca&lt;sup&gt;2+&lt;/sup&gt; Signaling in Astrocytes From Acute Brain Slices.

Journal: Bio-protocol

Authors' code: ladymariot/AstroResp (MIT)

Status: code verified, 5 files readable

Thursday, 3 July 2025 (1 paper)

[201] doi:10.1038/s42003-025-08435-8 [paper, repository]

Exposure to COVID-19 virus-like particles modulates firing patterns of cortical neurons in the mouse brain.

Journal: Communications biology

Authors' code: figshare 29238128 (CC-BY-4.0)

Status: code verified, 7 files readable, 2 matches

Wednesday, 2 July 2025 (1 paper)

[202] doi:10.1126/sciadv.adr6470 [paper, repository]

Simultaneous two-color imaging with a dual-channel miniscope in freely behaving mice.

Journal: Science advances

Authors' code: Aharoni-Lab/Miniscope-DAQ-QT-Software (GPL-3.0), denisecailab/ezTrack (GPL-3.0), denisecailab/Miniscope_2s-validation (no license)

Status: code verified, 254 files readable

Tuesday, 1 July 2025 (5 papers)

[203] doi:10.1038/s41467-025-60648-x [paper, repository]

Closed-loop two-photon functional imaging in a freely moving animal.

Journal: Nature communications

Authors' code: GershowLab/CRASH2p (gnu)

Status: code verified, 128 files readable, 4 matches

[204] doi:10.1038/s42003-025-08342-y [paper, repository]

Nascent actin dynamics and the disruption of calcium dynamics by actin arrest in developing neural cell networks.

Journal: Communications biology

Authors' code: SJG3/Coupled-Biomechanical-and-Ionic-Excitability-in-Developing-Neural-Cell-Networks_Code-Availability (GPL-3.0)

Status: code verified, 4 files readable, 3 matches

[205] doi:10.1038/s41598-025-05382-6 [paper, repository]

Intermingled representation of oral cavity in mouse trigeminal ganglion.

Journal: Scientific reports

Authors' code: pharmedku/trigeminal (no license)

Status: code verified

[206] doi:10.1002/cpz1.70161 [paper, repository]

PASTa: An Open-Source Analysis and Signal Processing Toolbox for Fiber Photometry Data.

Journal: Current protocols

Authors' code: rdonka/PASTa (no license)

Status: code verified, 71 files readable, 40 matches

[207] doi:10.1117/1.nph.12.3.035014 [paper, repository]

Depth-resolved fiber photometry of amyloid plaque signals in freely behaving Alzheimer's disease mice.

Journal: Neurophotonics

Authors' code: vsnnlab/AMaSiNe (no license)

Status: code verified, 16 files readable

Thursday, 19 June 2025 (1 paper)

[208] doi:10.1371/journal.pcbi.1012603 [paper, repository]

Predicting neuronal firing from calcium imaging using a control theoretic approach.

Journal: PLoS computational biology

Authors' code: N-Rondoni/slugFind (Apache-2.0)

Status: code verified, 35 files readable, 3 matches

Tuesday, 17 June 2025 (1 paper)

[209] doi:10.7554/elife.105422 [paper, repository]

A contextual fear conditioning paradigm in head-fixed mice exploring virtual reality.

Journal: eLife

Authors' code: seethakris/CFCMethodspaper (no license)

Status: code verified, 13 files readable, 2 matches

Wednesday, 11 June 2025 (3 papers)

[210] doi:10.1126/sciadv.ads4995 [paper, repository]

MiniXL: An open-source, large field-of-view epifluorescence miniscope enabling single-cell resolution and multi-region imaging in mice.

Journal: Science advances

Authors' code: Aharoni-Lab/Miniscope-LFOV (GPL-3.0)

Status: code verified, 944 files readable

[211] doi:10.1016/j.celrep.2025.115801 [paper, repository]

The amyloid precursor family of proteins in excitatory neurons are essential for regulating cortico-hippocampal circuit dynamics in vivo.

Journal: Cell reports

Authors' code: Zenodo 15210936 (CC-BY-4.0), petersaj/neuropixels_trajectory_explorer (GPL-3.0)

Status: code verified, 84 files readable, 8 matches

[212] doi:10.1016/j.celrep.2025.115814 [paper, repository]

Edinger-Westphal Urocortin-1 neurons regulate consumption and affect.

Journal: Cell reports

Authors' code: Zenodo 11624342 (CC-BY-4.0), SabrinaYuY/Fiber_photometry_data_analysis (MIT)

Status: code verified, 4 files readable, 2 matches

Tuesday, 10 June 2025 (1 paper)

[213] doi:10.3389/fphar.2025.1509837 [paper, data]

Kininogen enhances seizure susceptibility in mice possibly through bradykinin-induced modulation of calcium transients in glutamatergic and GABAergic neurons.

Journal: Frontiers in pharmacology

Status: data only, 2 datasets cited

Monday, 9 June 2025 (1 paper)

[214] doi:10.1016/j.crmeth.2025.101074 [paper, repository]

Preserving spatial and quantitative information in unpaired biomedical image-to-image translation.

Journal: Cell reports methods

Authors' code: figshare 28707146 (CC-BY-4.0), NICALab/STABLE (GPL-3.0), figshare 28936559 (CC-BY-4.0), NICALab/SUPPORT (GPL-3.0), google/in-silico-labeling (Apache-2.0), junyanz/pytorch-CycleGAN-and-pix2pix (BSD-3-Clause), NVlabs/MUNIT (CC-BY-NC-SA-4.0), Mid-Push/santa (MIT), cabooster/UTOM (GPL-3.0)

Status: code verified, 194 files readable, 5 matches

Sunday, 1 June 2025 (3 papers)

[215] doi:10.1093/g3journal/jkaf086 [paper, repository]

Neurons and molecules involved in noxious light sensation in Caenorhabditis elegans.

Journal: G3 (Bethesda, Md.)

Authors' code: micro-manager/mmcoreanddevices (no license), micro-manager.org (no license), Zenodo 13958554 (CC-BY-4.0)

Status: code verified, 1,681 files readable, 1 match

[216] doi:10.1002/cpz1.70167 [paper, repository]

Two-Photon Microscopy Functional Assays for Serial Imaging of Brain Microvessels and the Neurovascular Unit Through Disease Progression.

Journal: Current protocols

Authors' code: mcdowellkonnor/Vasometrics (no license)

Status: empty repository, 1 file readable

[217] doi:10.1117/1.nph.12.s2.s22803 [paper, data]

Brief disruptions in capillary flow result in rapid onset of hypoxia.

Journal: Neurophotonics

Status: data only, 1 dataset cited

Wednesday, 28 May 2025 (1 paper)

[218] doi:10.7554/elife.104914 [paper, repository]

Quantification of the effect of hemodynamic occlusion in two-photon imaging of mouse cortex.

Journal: eLife

Authors' code: Zenodo 15198651 (CC-BY-4.0), Zenodo 12632129 (CC-BY-4.0)

Status: code verified

Tuesday, 27 May 2025 (1 paper)

[219] doi:10.1016/j.isci.2025.112767 [paper, repository]

Microendoscopic calcium imaging in motor cortices of macaques during rest and movement.

Journal: iScience

Authors' code: Zenodo 15346239 (CC-BY-4.0)

Status: code verified, 3 files readable, 1 match

Monday, 26 May 2025 (1 paper)

[220] doi:10.1186/s12859-025-06150-z [paper, repository]

CRISP: correlation-refined image segmentation process.

Journal: BMC bioinformatics

Authors' code: computational-cell-analytics/micro-sam (MIT), jenniferkbriggs/CRISP (MIT)

Status: code verified, 285 files readable, 2 matches

Friday, 23 May 2025 (1 paper)

[221] doi:10.1038/s42003-025-08079-8 [paper, repository]

Three-photon in vivo imaging of neurons and glia in the medial prefrontal cortex with sub-cellular resolution.

Journal: Communications biology

Authors' code: FabrizioMusacchio/MotilA (GPL-3.0), Zenodo 15175054 (GPL-3.0)

Status: code verified, 35 files readable, 1 match

Thursday, 15 May 2025 (1 paper)

[222] doi:10.1016/j.celrep.2025.115717 [paper]

Optogenetic activation of cortical microglia promotes neuronal activity and pain hypersensitivity.

Journal: Cell reports

Status: code on request

Tuesday, 13 May 2025 (1 paper)

[223] doi:10.1073/pnas.2415268122 [paper, repository]

Split genetically encoded calcium indicators for interorganellar junctions.

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

Authors' code: doi:10.5061/dryad.5mkkwh7h4 (no license)

Status: code verified

Friday, 9 May 2025 (1 paper)

[224] doi:10.1101/2025.05.04.652136 [paper, repository]

A hierarchical adaptive optics strategy for three-photon imaging during behavior

Journal: bioRxiv (preprint)

Authors' code: aomicroscopy.org/dm-calib (no license), dop-oxford/dmlib (GPL-3.0), Zenodo 3714951 (CC-BY-4.0)

Status: code verified, 19 files readable, 2 matches

Wednesday, 7 May 2025 (1 paper)

[225] doi:10.1038/s41467-025-59530-7 [paper, repository]

A high-performance fluorescent sensor spatiotemporally reveals cell-type specific regulation of intracellular adenosine in vivo.

Journal: Nature communications

Authors' code: damiers/wave_analysis (GPL-3.0)

Status: code verified, 4 files readable, 1 match

Monday, 5 May 2025 (1 paper)

[226] doi:10.1016/j.xpro.2025.103800 [paper, repository]

Longitudinal calcium imaging of BNST neurons in mice during optogenetic manipulation of paraventricular thalamus axon terminals.

Journal: STAR protocols

Authors' code: Zenodo 13909372 (CC-BY-4.0), shihche0716/pva-ca-data-analysis (no license)

Status: code verified, 16 files readable, 2 matches

Friday, 2 May 2025 (1 paper)

[227] doi:10.7554/elife.101420 [paper, repository]

Aberration correction in long GRIN lens-based microendoscopes for extended field-of-view two-photon imaging in deep brain regions.

Journal: eLife

Authors' code: gitlab.iit.it/fellin-public/cite-on (Apache-2.0), gitlab.iit.it/chiara.nardin/longmicroendoscopes (GPL-3.0)

Status: code verified, 92 files readable, 16 matches

Wednesday, 30 April 2025 (1 paper)

[228] doi:10.1523/jneurosci.1187-24.2025 [paper, repository]

Spike Rate Inference from Mouse Spinal Cord Calcium Imaging Data.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Authors' code: HelmchenLabSoftware/Cascade (GPL-3.0)

Status: code verified, 20 files readable, 6 matches

Tuesday, 29 April 2025 (2 papers)

[229] doi:10.1371/journal.pbio.3003048 [paper, repository]

A sensitive soma-localized red fluorescent calcium indicator for in vivo imaging of neuronal populations at single-cell resolution.

Journal: PLoS biology

Authors' code: Shihao-Neuro/SomaFRCaMPi (MIT), Zenodo 14942673 (MIT)

Status: code verified, 45 files readable, 6 matches

[230] doi:10.1038/s41467-025-59303-2 [paper, repository]

Transparent, metal-free PEDOT:PSS neural interfaces for simultaneous recording of low-noise electrophysiology and artifact-free two-photon imaging.

Journal: Nature communications

Authors' code: Zenodo 14613681 (CC-BY-4.0)

Status: code verified, 2 files readable

Thursday, 24 April 2025 (1 paper)

[231] doi:10.21203/rs.3.rs-6306814/v1 [paper, repository]

Spike inference from calcium imaging data acquired with GCaMP8 indicators

Journal: Research Square (preprint)

Authors' code: helmchenlabsoftware/cascade (GPL-3.0), PTRRupprecht/Quantal-analysis-for-spike-inference (GPL-3.0), switch.ch/drive (no license)

Status: code verified, 30 files readable, 8 matches

Wednesday, 23 April 2025 (2 papers)

[232] doi:10.1016/j.cub.2025.03.039 [paper, data]

The neuropeptide FLP-11 induces and self-inhibits sleep through the receptor DMSR-1 in Caenorhabiditis elegans.

Journal: Current biology : CB

Status: data only, 1 dataset cited

[233] doi:10.3390/cosmetics12030086 [paper, data]

Kv1.3 Ion Channels Mediate Electrical Stimulation-Induced Collagen Expression in Human Dermal Fibroblasts.

Journal: Cosmetics

Status: code on request, 1 dataset cited

Friday, 18 April 2025 (1 paper)

[234] doi:10.1093/braincomms/fcaf153 [paper, repository]

Ongoing loss of viable neurons for weeks after mild hypoxia-ischaemia.

Journal: Brain communications

Authors' code: MGH-Epilepsy-Research-Group (no license)

Status: code verified

Tuesday, 15 April 2025 (1 paper)

[235] doi:10.1101/2025.04.08.647900 [paper, repository]

Depth-resolved fiber photometry of amyloid plaque signals in freely behaving Alzheimer’s disease mice

Journal: bioRxiv (preprint)

Authors' code: vsnnlab/AMaSiNe (no license)

Status: code verified, 16 files readable

Monday, 14 April 2025 (1 paper)

[236] doi:10.1021/acschemneuro.4c00632 [paper, repository]

Multi-Frequency Interpolation X-talk Removal Algorithm: Enabling Combinations of Concurrent Optogenetics and Lock-in Amplification Fiber Photometry via Removal of Optogenetic Stimulation Crosstalk.

Journal: ACS chemical neuroscience

Authors' code: maxbrkstone/mufix (no license)

Status: code verified, 26 files readable, 1 match

Friday, 11 April 2025 (1 paper)

[237] doi:10.1038/s41467-025-58817-z [paper, repository]

A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging.

Journal: Nature communications

Authors' code: doi:10.5061/dryad.crjdfn3ck (no license), CaliAli-PV/CaliAli (GPL-3.0), Zenodo 14934924 (GPL-3.0)

Status: code verified, 1,342 files readable, 11 matches

Tuesday, 8 April 2025 (1 paper)

[238] doi:10.1038/s41467-025-58661-1 [paper, repository]

Discrete photoentrainment of mammalian central clock is regulated by bi-stable dynamic network in the suprachiasmatic nucleus.

Journal: Nature communications

Authors' code: chenwunci/motion_correction_2D (no license)

Status: code verified, 7 files readable

Friday, 4 April 2025 (1 paper)

[239] doi:10.1016/j.crmeth.2025.101010 [paper]

Minimally invasive, wide-field two-photon imaging of the brainstem at cellular resolution.

Journal: Cell reports methods

Status: code on request

Wednesday, 2 April 2025 (1 paper)

[240] doi:10.1113/jp286407 [paper, repository]

Activation of TRPA1 and TRPM3 triggers Ca&lt;sup&gt;2+&lt;/sup&gt; waves in central terminals of sensory neurons and facilitates synaptic activity in the spinal dorsal horn.

Journal: The Journal of physiology

Authors' code: Zenodo 14752276 (MIT)

Status: code verified, 25 files readable

Tuesday, 1 April 2025 (6 papers)

[241] doi:10.1002/cne.70046 [paper, repository]

Evidence for Auditory Stimulus-Specific Adaptation But Not Deviance Detection in Larval Zebrafish Brains.

Journal: The Journal of comparative neurology

Authors' code: stednitzs/oddball (no license)

Status: code verified, 8 files readable

[242] doi:10.7554/elife.104469 [paper, repository]

Peripheral opioid receptor antagonism alleviates fentanyl-induced cardiorespiratory depression and is devoid of aversive behavior.

Journal: eLife

Authors' code: Zenodo 15042135 (Apache-2.0), jessinbotham/ruyle_photometry (Apache-2.0)

Status: code verified, 10 files readable, 1 match

[243] doi:10.1073/pnas.2410101122 [paper, data]

Reactivation of memory-associated neurons induces downstream suppression of competing neuronal populations.

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

Status: data only, 1 dataset cited

[244] doi:10.1117/1.nph.12.2.025013 [paper, repository]

Compressive streak microscopy for fast sampling of fluorescent reporters of neural activity.

Journal: Neurophotonics

Authors' code: caichangjia/compressive_streak_microscopy (GPL-2.0)

Status: code verified, 19 files readable, 14 matches

[245] doi:10.1117/1.nph.12.2.025016 [paper]

Two-photon fiberscope with a proactive optoelectrical commutator for rotational resistance-free imaging in freely behaving rodents.

Journal: Neurophotonics

Status: code on request

[246] doi:10.1117/1.nph.12.2.025018 [paper]

Wide-field fluorescence navigation system for efficient miniature multiphoton imaging in freely behaving animals.

Journal: Neurophotonics

Status: code on request

Monday, 31 March 2025 (1 paper)

[247] doi:10.1117/1.nph.12.2.025003 [paper, repository]

Obtaining artifact-corrected signals in fiber photometry via isosbestic signals, robust regression, and dF/F calculations.

Journal: Neurophotonics

Authors' code: philjrdb/RegressionSim (no license), OSF z6c5b (no license)

Status: code verified, 15 files readable, 8 matches

Saturday, 29 March 2025 (1 paper)

[248] doi:10.1117/1.jbo.30.4.046002 [paper]

Deep structural brain imaging via computational three-photon microscopy.

Journal: Journal of biomedical optics

Status: code on request

Thursday, 27 March 2025 (1 paper)

[249] doi:10.1016/j.neuron.2025.03.006 [paper]

Vascular motion in the dorsal root ganglion sensed by Piezo2 in sensory neurons triggers episodic pain.

Journal: Neuron

Status: code on request

Tuesday, 25 March 2025 (1 paper)

[250] doi:10.1117/1.nph.12.2.025001 [paper]

Shallow-angle intracranial cannula for repeated infusion and &lt;i&gt;in vivo&lt;/i&gt; imaging with multiphoton microscopy.

Journal: Neurophotonics

Status: code on request

Thursday, 20 March 2025 (1 paper)

[251] doi:10.1016/j.isci.2025.112256 [paper, repository]

Atypical plume-like events contribute to glutamate accumulation in metabolic stress conditions.

Journal: iScience

Authors' code: gitlab.utwente.nl/m7686441/focalglutamate_modelsimulations (no license)

Status: code verified, 8 files readable, 2 matches

Friday, 14 March 2025 (1 paper)

[252] doi:10.7554/elife.93063 [paper, repository]

Microprism-based two-photon imaging of the mouse inferior colliculus reveals novel organizational principles of the auditory midbrain.

Journal: eLife

Authors' code: doi:10.5061/dryad.v41ns1s70 (no license), Zenodo 14946966 (MIT)

Status: code verified, 47 files readable, 6 matches

Wednesday, 12 March 2025 (1 paper)

[253] doi:10.7554/elife.95802 [paper, repository]

A statistical framework for analysis of trial-level temporal dynamics in fiber photometry experiments.

Journal: eLife

Authors' code: gloewing/fastFMM (no license), gloewing/photometry_fLMM (CC0-1.0)

Status: code verified, 69 files readable, 24 matches

Tuesday, 11 March 2025 (2 papers)

[254] doi:10.7554/elife.90511 [paper, repository]

A neural correlate of individual odor preference in &lt;i&gt;Drosophila&lt;/i&gt;.

Journal: eLife

Authors' code: Zenodo 14252278 (CC-BY-4.0)

Status: code verified

[255] doi:10.3389/fncel.2025.1558504 [paper, repository]

Characterize neuronal responses to natural movies in the mouse superior colliculus.

Journal: Frontiers in cellular neuroscience

Authors' code: yatangli/Li_NaturalMovies_2025 (Apache-2.0)

Status: code verified, 4 files readable, 5 matches

Saturday, 8 March 2025 (1 paper)

[256] doi:10.1016/j.celrep.2025.115391 [paper, repository]

Erasable hippocampal neural signatures predict memory discrimination.

Journal: Cell reports

Authors' code: wmau/FearReinstatement (no license), nkinsky/Eraser (GPL-3.0), nkinsky/ImageCamp (no license), soberlab/Hierarchical-Bootstrap-Paper (GPL-3.0)

Status: code verified, 831 files readable, 15 matches

Saturday, 1 March 2025 (1 paper)

[257] doi:10.1111/ejn.70036 [paper]

Olfactory Receptor Responses to Pure Odorants in Drosophila melanogaster.

Journal: The European journal of neuroscience

Status: code on request

Tuesday, 25 February 2025 (2 papers)

[258] doi:10.1186/s13041-025-01188-9 [paper, data]

Roles of mediodorsal thalamus in observational fear-related neural activity in mouse anterior cingulate cortex.

Journal: Molecular brain

Status: data only, 1 dataset cited

[259] doi:10.1097/j.pain.0000000000003512 [paper, repository]

Modelling inflammation-induced peripheral sensitization in a dish-more complex than expected?

Journal: Pain

Authors' code: Zenodo 12783430 (CC-BY-4.0), Zenodo 13122856 (CC-BY-4.0)

Status: code verified, 1 file readable

Friday, 21 February 2025 (1 paper)

[260] doi:10.1038/s41598-025-90878-4 [paper, repository]

Dynamic changes in cortical neurotrophic factor-positive interneurons during sleep.

Journal: Scientific reports

Authors' code: christinemlmuheim/NDNF-INs-and-Sleep (MIT)

Status: code verified, 3 files readable, 2 matches

Thursday, 20 February 2025 (1 paper)

[261] doi:10.1038/s41592-025-02610-9 [paper, repository]

Genetically encoded biosensor for fluorescence lifetime imaging of PTEN dynamics in the intact brain.

Journal: Nature methods

Authors' code: ryoheiyasuda/FLIMage_public (no license), schollben/imaging (no license)

Status: code verified, 363 files readable, 4 matches

Monday, 17 February 2025 (1 paper)

[262] doi:10.3389/fnsyn.2025.1548563 [paper, repository]

Postsynaptic spiking determines anti-Hebbian LTD in visual cortex basket cells.

Journal: Frontiers in synaptic neuroscience

Authors' code: pj-sjostrom/MultiPatch (GPL-3.0), pj-sjostrom/jScan (no license), pj-sjostrom/LineScanAnalysis (AGPL-3.0), pj-sjostrom/qMorph (GPL-3.0)

Status: code verified, 8 files readable

Wednesday, 12 February 2025 (1 paper)

[263] doi:10.1523/eneuro.0025-24.2024 [paper, repository]

FAST: Fast, Free, Consistent, and Unsupervised Oligodendrocyte Segmentation and Tracking System.

Journal: eNeuro

Authors' code: PennSIVE/bossr (other)

Status: code verified, 26 files readable, 3 matches

Tuesday, 11 February 2025 (1 paper)

[264] doi:10.1016/j.celrep.2025.115292 [paper, repository]

Higher-order thalamic input to cortex selectively conveys state information.

Journal: Cell reports

Authors' code: cardin-higley-lab/CC_TC_Neske_Project (no license), Zenodo 13899503 (CC-BY-4.0)

Status: code verified, 886 files readable

Saturday, 1 February 2025 (1 paper)

[265] doi:10.1093/cercor/bhaf007 [paper]

Developmental maturation of millimeter-scale functional networks across brain areas.

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

Status: code on request

Thursday, 30 January 2025 (2 papers)

[266] doi:10.1073/pnas.2416214122 [paper, repository]

Impaired spatial coding of the hippocampus in a dentate gyrus hypoplasia mouse model.

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

Authors' code: KordingLab/Neural_Decoding (BSD-3-Clause), XiaojingChenLab/DGless (no license)

Status: code verified, 32 files readable

[267] doi:10.1016/j.bpsgos.2025.100455 [paper, repository]

Diminished Social Memory and Hippocampal Correlates of Social Interactions in Chronic Social Defeat Stress Susceptibility.

Journal: Biological psychiatry global open science

Authors' code: tpwonglab/social-ensemble-analysis (CC-BY-4.0)

Status: code verified, 6 files readable

Wednesday, 29 January 2025 (1 paper)

[268] doi:10.1186/s40478-024-01920-x [paper]

Understanding retinal tau pathology through functional 2D and 3D iPSC-derived in vitro retinal models.

Journal: Acta neuropathologica communications

Status: code on request

Tuesday, 28 January 2025 (1 paper)

[269] doi:10.1038/s41467-025-56289-9 [paper, repository]

Sub-cellular population imaging tools reveal stable apical dendrites in hippocampal area CA3.

Journal: Nature communications

Authors' code: Zenodo 14207307 (CC-BY-4.0), basulab-nyu/d-NMF (GPL-3.0)

Status: code verified, 34 files readable, 7 matches

Friday, 24 January 2025 (1 paper)

[270] doi:10.1186/s13041-025-01177-y [paper, data]

Surgery impairs glymphatic activity and cognitive function in aged mice.

Journal: Molecular brain

Status: data only, 1 dataset cited

Monday, 20 January 2025 (1 paper)

[271] doi:10.1186/s40708-024-00248-5 [paper, repository]

CalciumZero: a toolbox for fluorescence calcium imaging on iPSC derived brain organoids.

Journal: Brain informatics

Authors' code: CanYing0913/CalciumZero (no license)

Status: code verified, 21 files readable, 1 match

Friday, 17 January 2025 (1 paper)

[272] doi:10.1016/j.crmeth.2024.100964 [paper, repository]

Unifying community whole-brain imaging datasets enables robust neuron identification and reveals determinants of neuron position in C. elegans.

Journal: Cell reports methods

Authors' code: yemini-lab/neuropal_id (CC-BY-NC-SA-4.0), focolab/eats-worm (MIT), wormid.org (no license), Zenodo 13910335 (CC-BY-4.0), focolab/ndx-multichannel-volume (BSD-3-Clause), Zenodo 13906028 (CC-BY-NC-4.0), Zenodo 13905893 (CC-BY-NC-4.0), Zenodo 13910463 (CC-BY-4.0), XinweiYu/fDNC_Neuron_ID (no license), amin-nejat/stat-atlas (no license), lu-lab/CRF_Cell-ID (no license), Zenodo 3692138 (Apache-2.0), focolab/NWBelegans (no license), dandi/dandi-cli (Apache-2.0)

Status: code verified, 1,218 files readable, 18 matches

Wednesday, 15 January 2025 (3 papers)

[273] doi:10.1523/eneuro.0363-24.2024 [paper, repository]

Fxr1 Deletion from Cortical Parvalbumin Interneurons Modifies Their Excitatory Synaptic Responses.

Journal: eNeuro

Authors' code: ksscheuer/FXR1 (no license), Zenodo 14342804 (CC-BY-4.0), ksscheuer/Inter_intra_laminar (no license), Zenodo 11106962 (CC-BY-4.0)

Status: code verified, 6 files readable, 1 match

[274] doi:10.1113/jp286631 [paper]

In vivo calcium imaging reveals directional sensitivity of C-low threshold mechanoreceptors.

Journal: The Journal of physiology

Status: code on request

[275] doi:10.3390/insects16010084 [paper, data]

Differential Coding of Fruit, Leaf, and Microbial Odours in the Brains of <i>Drosophila suzukii</i> and <i>Drosophila melanogaster</i>.

Journal: Insects

Status: data only, 1 dataset cited

Friday, 10 January 2025 (1 paper)

[276] doi:10.1002/jbio.202400513 [paper, data]

Neuronal Imaging at 8-Bit Depth to Combine High Spatial and High Temporal Resolution With Acquisition Rates Up To 40 kHz.

Journal: Journal of biophotonics

Status: data only, 2 datasets cited

Thursday, 9 January 2025 (1 paper)

[277] doi:10.7554/elife.98742 [paper, repository]

Nitric oxide modulates contrast suppression in a subset of mouse retinal ganglion cells.

Journal: eLife

Authors' code: datajoint.github.io (no license), eulerlab/nitric_oxide_rgc_eLife (MIT), doi:10.12751/g-node.mpf63w (no license)

Status: code verified, 29 files readable, 4 matches

Wednesday, 8 January 2025 (2 papers)

[278] doi:10.1126/sciadv.adp5763 [paper, data]

Photophysics-informed two-photon voltage imaging using FRET-opsin voltage indicators.

Journal: Science advances

Status: data only, 1 dataset cited

[279] doi:10.7554/elife.100856 [paper, data]

Multi-dimensional oscillatory activity of mouse GnRH neurons in vivo.

Journal: eLife

Status: data only, 1 dataset cited

Tuesday, 7 January 2025 (2 papers)

[280] doi:10.1073/pnas.2410433122 [paper, data]

A synapse-specific refractory period for plasticity at individual dendritic spines.

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

Status: data only, 1 dataset cited

[281] doi:10.1016/j.nbd.2025.106795 [paper]

Cerebral cortical functional hyperconnectivity in a mouse model of spinocerebellar ataxia type 8 (SCA8).

Journal: Neurobiology of disease

Status: code on request

Wednesday, 1 January 2025 (7 papers)

[282] doi:10.1111/micc.70001 [paper, repository]

Combining In Vivo Two-Photon and Laser Speckle Microscopy With the Ex Vivo Capillary-Parenchymal Arteriole Preparation as a Novel Approach to Study Neurovascular Coupling.

Journal: Microcirculation (New York, N.Y. : 1994)

Authors' code: JiLabUCBerkeley/FACED2PFM-vessel (no license)

Status: code verified, 46 files readable

[283] doi:10.1002/cpz1.70090 [paper, repository]

Miniscope Imaging of Nucleus Accumbens Neural Activity in Freely Behaving Rats: Virus Injection, Gradient Index Lens Implantation, Recording Strategies, and Analytical Methods.

Journal: Current protocols

Authors' code: njbeacher/njbeacher.github.io (MIT)

Status: empty repository, 2 files readable

[284] doi:10.1111/ejn.16657 [paper, data]

Fast Neuronal Calcium Signals in Brain Slices Loaded With Fluo-4 AM Ester.

Journal: The European journal of neuroscience

Status: data only, 1 dataset cited

[285] doi:10.1117/1.nph.12.s1.s14606 [paper, repository]

Neurovascular coupling over cortical brain areas and resting state network connectivity with and without rigidified carotid artery.

Journal: Neurophotonics

Authors' code: marl1bakker/CaCl_P2 (no license)

Status: code verified, 80 files readable, 10 matches

[286] doi:10.1117/1.nph.12.s1.s14613 [paper]

Repetitive transcranial magnetic stimulation increases synaptic plasticity of cortical axons in the APP/PS1 amyloidosis mouse model.

Journal: Neurophotonics

Status: code on request

[287] doi:10.1109/tnsre.2025.3586175 [paper, repository]

Behavioral Classification of Sequential Neural Activity Using Time Varying Recurrent Neural Networks.

Journal: IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society

Authors' code: saxenalab-neuro/TV_RNN (no license)

Status: code verified, 8 files readable

[288] doi:10.1117/1.nph.12.s1.s14616 [paper, repository]

Bridging the gap: umIT makes complex imaging data accessible to scientists of all backgrounds.

Journal: Neurophotonics

Authors' code: labeotech.github.io/umit (no license), LabeoTech/Umit (GPL-3.0)

Status: code verified, 362 files readable, 5 matches

Friday, 27 December 2024 (1 paper)

[289] doi:10.1088/1741-2552/ada0eb [paper, data]

Longitudinal changes in electrophysiology and widefield calcium imaging following electrode implantation.

Journal: Journal of neural engineering

Status: data only, 1 dataset cited

Tuesday, 24 December 2024 (1 paper)

[290] doi:10.3390/s25010004 [paper]

A Flexible, Implantable, Bioelectronic Electroporation Device for Targeted Ablation of Seizure Foci in the Mouse Brain.

Journal: Sensors (Basel, Switzerland)

Status: code on request

Monday, 23 December 2024 (1 paper)

[291] doi:10.1371/journal.pcbi.1012655 [paper, repository]

Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling.

Journal: PLoS computational biology

Authors' code: monet-yonsei/mmsdcm (no license)

Status: code verified, 31 files readable, 15 matches

Friday, 20 December 2024 (1 paper)

[292] doi:10.1016/j.xpro.2024.103534 [paper]

Protocol for in vivo recording of neural activity in deep structures of mice brain via gradient lenses by calcium imaging.

Journal: STAR protocols

Status: code on request

Wednesday, 18 December 2024 (1 paper)

[293] doi:10.1186/s13041-024-01168-5 [paper, repository]

Dynamic changes in the hippocampal neuronal circuits activity following acute stress revealed by miniature fluorescence microscopy imaging.

Journal: Molecular brain

Authors' code: spbstu-applied-math/NeuroActivityToolkit (no license)

Status: code verified, 17 files readable, 5 matches

Friday, 13 December 2024 (1 paper)

[294] doi:10.1371/journal.pone.0309366 [paper, data]

Longitudinal imaging of the taste bud in vivo with two-photon laser scanning microscopy.

Journal: PloS one

Status: data only, 3 datasets cited

Tuesday, 10 December 2024 (1 paper)

[295] doi:10.1172/jci.insight.181783 [paper]

Noise induces Ca2+ signaling waves and Chop/S-Xbp1 expression in the hearing cochlea.

Journal: JCI insight

Status: code on request

Monday, 9 December 2024 (1 paper)

[296] doi:10.3389/fnins.2024.1445020 [paper, repository]

Imaging distinct neuronal populations with a dual channel miniscope.

Journal: Frontiers in neuroscience

Authors' code: liang-bo/AutoStereota (MIT)

Status: code verified, 16 files readable, 1 match

Wednesday, 4 December 2024 (1 paper)

[297] doi:10.1038/s44303-024-00055-x [paper, repository]

Robust self-supervised denoising of voltage imaging data using CellMincer.

Journal: Npj imaging

Authors' code: cellarium-ai/CellMincerPaperAnalysis (no license), cellarium-ai/CellMincer (BSD-3-Clause), cellarium-ai/Optosynth (BSD-3-Clause)

Status: code verified, 49 files readable, 18 matches

Friday, 22 November 2024 (1 paper)

[298] doi:10.1113/ep092219 [paper, repository]

Imaging the large-scale and cellular response to focal traumatic brain injury in mouse neocortex.

Journal: Experimental physiology

Authors' code: margolislab/Bibineyshvili_2024 (GPL-3.0)

Status: code verified, 13 files readable

Thursday, 21 November 2024 (1 paper)

[299] doi:10.1038/s41467-024-54320-z [paper, repository]

Early and late place cells during postnatal development of the hippocampus.

Journal: Nature communications

Authors' code: XiaojingChenLab/EarlyPlaceCell (no license), Zenodo 13911919 (CC-BY-4.0)

Status: code verified, 1 file readable

Monday, 11 November 2024 (1 paper)

[300] doi:10.1038/s44319-024-00309-0 [paper, data]

Experience-driven development of decision-related representations in the auditory cortex.

Journal: EMBO reports

Status: data only, 1 dataset cited

Tuesday, 5 November 2024 (1 paper)

[301] doi:10.1038/s41467-024-53685-5 [paper, repository]

Fast and light-efficient remote focusing for volumetric voltage imaging.

Journal: Nature communications

Authors' code: danionella/Bohm_et_al_2024 (no license)

Status: code verified, 16 files readable, 1 match

Friday, 1 November 2024 (1 paper)

[302] doi:10.1016/j.isci.2024.111298 [paper, repository]

Evaluating chemical effects on human neural cells through calcium imaging and deep learning.

Journal: iScience

Authors' code: BansalAnkush/Chemical-Effects-on-NPCs (no license)

Status: code verified, 7 files readable, 3 matches

Tuesday, 29 October 2024 (1 paper)

[303] doi:10.1117/1.nph.11.4.045007 [paper, repository]

DeepVID v2: self-supervised denoising with decoupled spatiotemporal enhancement for low-photon voltage imaging.

Journal: Neurophotonics

Authors' code: bu-cisl/DeepVIDv2 (GPL-3.0)

Status: code verified, 11 files readable, 1 match

Friday, 25 October 2024 (1 paper)

[304] doi:10.1007/s00018-024-05475-x [paper, data]

Human TRPV1 is an efficient thermogenetic actuator for chronic neuromodulation.

Journal: Cellular and molecular life sciences : CMLS

Status: data only, 1 dataset cited

Tuesday, 22 October 2024 (1 paper)

[305] doi:10.1016/j.heliyon.2024.e39574 [paper, repository]

Automated denoising software for calcium imaging signals using deep learning.

Journal: Heliyon

Authors' code: SharifAmit/CalDenoise (BSD-3-Clause)

Status: code verified, 29 files readable, 7 matches

Saturday, 19 October 2024 (1 paper)

[306] doi:10.1038/s41598-024-75170-1 [paper, repository]

Hippocampal recording with a soft microelectrode array in a cranial window imaging scheme: a validation study.

Journal: Scientific reports

Authors' code: BenceSzmola/DataAnalysisSuite (no license)

Status: code verified, 54 files readable

Friday, 18 October 2024 (1 paper)

[307] doi:10.1016/j.xpro.2024.103407 [paper, repository]

Protocol for synchronized wireless fiber photometry and video recordings in rodents during behavior.

Journal: STAR protocols

Authors' code: Zenodo 10819265 (CC-BY-4.0)

Status: code verified, 3 files readable, 3 matches

Thursday, 17 October 2024 (1 paper)

[308] doi:10.1016/j.xcrm.2024.101781 [paper, repository]

Neuropeptide therapeutics to repress lateral septum neurons that disable sociability in an autism mouse model.

Journal: Cell reports. Medicine

Authors' code: PHYSIOPATHOLOGIE-RYTHME-CARDIAQUE/Photometry (GPL-3.0)

Status: code verified, 13 files readable, 1 match

Wednesday, 16 October 2024 (2 papers)

[309] doi:10.1523/eneuro.0079-24.2024 [paper, repository]

NeuroART: Real-Time Analysis and Targeting of Neuronal Population Activity during Calcium Imaging for Informed Closed-Loop Experiments.

Journal: eNeuro

Authors' code: losertlab/NeuroART (no license)

Status: code verified, 1,804 files readable, 11 matches

[310] doi:10.1186/s13293-024-00653-9 [paper, repository]

Sex differences in prelimbic cortex calcium dynamics during stress and fear learning.

Journal: Biology of sex differences

Authors' code: Anderolab/Anderolab (no license)

Status: code verified, 85 files readable, 4 matches

Friday, 11 October 2024 (1 paper)

[311] doi:10.1016/j.celrep.2024.114813 [paper, repository]

The medial entorhinal cortex encodes multisensory spatial information.

Journal: Cell reports

Authors' code: Zenodo 13737336 (CC-BY-4.0), Zenodo 13737335 (CC-BY-4.0), gulab-nih/nguyenetalcellreports2024 (no license)

Status: code verified, 84 files readable, 1 match

Friday, 4 October 2024 (1 paper)

[312] doi:10.1038/s42003-024-06731-3 [paper]

Two-photon all-optical neurophysiology for the dissection of larval zebrafish brain functional and effective connectivity.

Journal: Communications biology

Status: code on request

Tuesday, 1 October 2024 (2 papers)

[313] doi:10.1093/genetics/iyae125 [paper, data]

Adapting and optimizing GCaMP8f for use in Caenorhabditis elegans.

Journal: Genetics

Status: data only, 1 dataset cited

[314] doi:10.1117/1.nph.11.4.045010 [paper]

Mapping multi-regional functional connectivity of astrocyte-neuronal networks during behaviors.

Journal: Neurophotonics

Status: code on request

Monday, 30 September 2024 (1 paper)

[315] doi:10.1016/j.xpro.2024.103331 [paper, repository]

Protocol for an open-source system to integrate calcium imaging, pupillometry, and locomotion-estimated tracking in head-fixed mice.

Journal: STAR protocols

Authors' code: UNC-optics/CaPuLeT (no license)

Status: code verified, 7 files readable, 6 matches

Friday, 27 September 2024 (1 paper)

[316] doi:10.1038/s41598-024-73577-4 [paper]

Infrared neuroglial modulation of spinal locomotor networks.

Journal: Scientific reports

Status: code on request

Tuesday, 24 September 2024 (1 paper)

[317] doi:10.1523/eneuro.0003-24.2024 [paper]

MeCP2 Deficiency Alters the Response Selectivity of Prefrontal Cortical Neurons to Different Social Stimuli.

Journal: eNeuro

Status: code on request

Tuesday, 17 September 2024 (1 paper)

[318] doi:10.1371/journal.pone.0308573 [paper, data]

Region of interest determination algorithm of lensless calcium imaging datasets.

Journal: PloS one

Status: data only, 1 dataset cited

Monday, 16 September 2024 (1 paper)

[319] doi:10.1038/s41467-024-52397-0 [paper, repository]

In vivo imaging of vagal-induced myenteric plexus responses in gastrointestinal tract with an optical window.

Journal: Nature communications

Authors' code: scidb.cn/s/7jjni2 (no license)

Status: code verified

Friday, 13 September 2024 (1 paper)

[320] doi:10.1016/j.celrep.2024.114723 [paper]

Spatiotemporal relationships between neuronal, metabolic, and hemodynamic signals in the awake and anesthetized mouse brain.

Journal: Cell reports

Status: code on request

Thursday, 12 September 2024 (2 papers)

[321] doi:10.1002/adhm.202402132 [paper, repository]

Dye-Based Fluorescent Organic Nanoparticles, New Promising Tools for Optogenetics.

Journal: Advanced healthcare materials

Authors' code: LAGONteam/PyTwoPhotonExcitedFluorescence (no license)

Status: code verified, 26 files readable, 1 match

[322] doi:10.1016/j.xpro.2024.103305 [paper, repository]

STARDUST: A pipeline for the unbiased analysis of astrocyte regional calcium dynamics.

Journal: STAR protocols

Authors' code: papouinlab/STARDUST (GPL-3.0)

Status: code verified, 8 files readable, 40 matches

Wednesday, 11 September 2024 (1 paper)

[323] doi:10.1021/acsphotonics.4c00111 [paper, data]

Deep Mouse Brain Two-Photon Near-Infrared Fluorescence Imaging Using a Superconducting Nanowire Single-Photon Detector Array.

Journal: ACS photonics

Status: data only, 1 dataset cited

Tuesday, 10 September 2024 (1 paper)

[324] doi:10.1038/s41467-024-51432-4 [paper, repository]

Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysis.

Journal: Nature communications

Authors' code: prevedel-lab/AO (no license), prevedel-lab/Deep3P-Denoising (GPL-3.0), Zenodo 11175040 (CC-BY-4.0)

Status: code verified, 30 files readable, 8 matches

Friday, 6 September 2024 (1 paper)

[325] doi:10.1038/s41467-024-51816-6 [paper, repository]

Wide-field calcium imaging of cortical activation and functional connectivity in externally- and internally-driven locomotion.

Journal: Nature communications

Authors' code: west0883/calcium_imaging_of_externally_and_internally_driven_locomotion (no license), Zenodo 12688490 (CC-BY-4.0)

Status: code verified, 1,086 files readable, 19 matches

Thursday, 5 September 2024 (2 papers)

[326] doi:10.7554/elife.93789 [paper, repository]

Analysis of fast calcium dynamics of honey bee olfactory coding.

Journal: eLife

Authors' code: mp599/2024_elife (MIT)

Status: code verified, 7 files readable, 7 matches

[327] doi:10.1073/pnas.2321021121 [paper, data]

Capillary regression leads to sustained local hypoperfusion by inducing constriction of upstream transitional vessels.

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

Status: data only, 1 dataset cited

Wednesday, 28 August 2024 (2 papers)

[328] doi:10.7554/elife.96534 [paper, repository]

Sex-dependent, lateralized engagement of anterior insular cortex inputs to the dorsolateral striatum in binge alcohol drinking.

Journal: eLife

Authors' code: dlhagger/AIC_Fiber_Photometry (MIT)

Status: code verified, 3 files readable, 1 match

[329] doi:10.1126/sciadv.adj2547 [paper, repository]

Cl&lt;sup&gt;-&lt;/sup&gt;-dependent amplification of excitatory synaptic potentials at distal dendrites revealed by voltage imaging.

Journal: Science advances

Authors' code: nb.biophys.kyoto-u.ac.jp/model (no license), supp:PMC11352850/sciadv.adj2547_supplementary_code.zip (no license)

Status: code verified, 16 files readable, 3 matches

Tuesday, 20 August 2024 (1 paper)

[330] doi:10.1038/s41598-024-70014-4 [paper, repository]

The recovery of parabolic avalanches in spatially subsampled neuronal networks at criticality.

Journal: Scientific reports

Authors' code: PlenzLab/ParabolicAvalanches (MIT)

Status: code verified, 6 files readable

Wednesday, 14 August 2024 (2 papers)

[331] doi:10.1038/s41586-024-07915-x [paper, repository]

Causal evidence of a line attractor encoding an affective state.

Journal: Nature

Authors' code: lindermanlab/ssm (MIT)

Status: code verified, 67 files readable, 2 matches

[332] doi:10.1016/j.jneumeth.2024.110250 [paper, repository]

Attention-based CNN-BiLSTM for sleep state classification of spatiotemporal wide-field calcium imaging data.

Journal: Journal of neuroscience methods

Authors' code: comp-imaging-sci/attention-based-bilstm-sleep-scoring (MIT)

Status: code verified, 20 files readable, 8 matches

Friday, 9 August 2024 (1 paper)

[333] doi:10.1038/s42003-024-06668-7 [paper, repository]

Accurate neuron segmentation method for one-photon calcium imaging videos combining convolutional neural networks and clustering.

Journal: Communications biology

Authors' code: JinghaoLu/MIN1PIPE (GPL-3.0), zhoupc/CNMF_E (GPL-3.0), schnitzer-lab/EXTRACT-public (MIT), yuanlong-o/Deep_widefield_cal_inferece (GPL-2.0), YijunBao/SUNS2_ANE_paper_reproduction (GPL-2.0), Zenodo 12742872 (CC-BY-4.0)

Status: code verified, 1,518 files readable, 22 matches

Thursday, 1 August 2024 (1 paper)

[334] doi:10.1371/journal.pone.0307962 [paper, repository]

Intravital two-photon microscopy of the native mouse thymus.

Journal: PloS one

Authors' code: SpencerLab-BIO/NativeThymusScripts (CC0-1.0)

Status: code verified, 10 files readable

Tuesday, 30 July 2024 (1 paper)

[335] doi:10.1038/s41467-024-50821-z [paper, repository]

Large-scale calcium imaging reveals a systematic V4 map for encoding natural scenes.

Journal: Nature communications

Authors' code: Zenodo 10972034 (CC-BY-4.0)

Status: code verified, 12 files readable, 1 match

Friday, 26 July 2024 (1 paper)

[336] doi:10.1038/s41467-024-50306-z [paper, repository]

Demixing fluorescence time traces transmitted by multimode fibers.

Journal: Nature communications

Authors' code: comediaLKB/DemixedFiberPhotometry (GPL-3.0), RimoliCV/NMF_DemixedFiberPhotometry (GPL-3.0), laboGigan/SpeckledNeuronsControl (GPL-3.0), Zenodo 12125030 (CC-BY-4.0)

Status: code verified, 23 files readable, 4 matches

Tuesday, 23 July 2024 (1 paper)

[337] doi:10.7554/elife.93804 [paper, repository]

Aberrant hippocampal Ca²⁺ microwaves following synapsin-dependent adeno-associated viral expression of Ca²⁺ indicators.

Journal: eLife

Authors' code: tonykelly00/Ca_waves_data-Elife (no license)

Status: code verified, 4 files readable

Monday, 22 July 2024 (1 paper)

[338] doi:10.7554/elife.93983 [paper, repository]

Neural activity ramps in frontal cortex signal extended motivation during learning.

Journal: eLife

Authors' code: Zenodo 11451977 (CC-BY-4.0), RajasethupathyLabGitHub/RegaladoElifePaperCode (no license)

Status: code verified, 25 files readable, 1 match

Friday, 19 July 2024 (2 papers)

[339] doi:10.1186/s11658-024-00619-0 [paper, data]

Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.

Journal: Cellular & molecular biology letters

Status: data only, 1 dataset cited

[340] doi:10.1016/j.isci.2024.110554 [paper, repository]

Long-working-distance high-collection-efficiency three-photon microscopy for <i>in vivo</i> long-term imaging of zebrafish and organoids.

Journal: iScience

Authors' code: AllenInstitute/deepinterpolation (BSD-2-Clause), AdaptiveMotorControlLab/CEBRA (Apache-2.0)

Status: code verified, 164 files readable, 1 match

Thursday, 11 July 2024 (1 paper)

[341] doi:10.7554/elife.93498 [paper, repository]

Clustered synapses develop in distinct dendritic domains in visual cortex before eye opening.

Journal: eLife

Authors' code: figshare 22674748 (CC-BY-4.0)

Status: code verified, 37 files readable, 7 matches

Wednesday, 10 July 2024 (2 papers)

[342] doi:10.1038/s41467-024-50153-y [paper, data]

β-amyloid monomer scavenging by an anticalin protein prevents neuronal hyperactivity in mouse models of Alzheimer's Disease.

Journal: Nature communications

Status: data only, 1 dataset cited

[343] doi:10.1038/s41565-024-01711-4 [paper]

Graphene oxide electrodes enable electrical stimulation of distinct calcium signalling in brain astrocytes.

Journal: Nature nanotechnology

Status: code on request

Monday, 8 July 2024 (1 paper)

[344] doi:10.1523/eneuro.0007-24.2024 [paper]

Trauma in Neonatal Acute Brain Slices Alters Calcium and Network Dynamics and Causes Calpain-Mediated Cell Death.

Journal: eNeuro

Status: code on request

Friday, 5 July 2024 (1 paper)

[345] doi:10.1523/eneuro.0438-23.2024 [paper, repository]

Cell-Specific Single Viral Vector CRISPR/Cas9 Editing and Genetically Encoded Tool Delivery in the Central and Peripheral Nervous Systems.

Journal: eNeuro

Authors' code: jamiecm17/CRISPR-Cas9-Paper (no license)

Status: code verified, 3 files readable, 2 matches

Tuesday, 2 July 2024 (1 paper)

[346] doi:10.1038/s41467-024-49442-3 [paper, repository]

A chemogenetic approach for dopamine imaging with tunable sensitivity.

Journal: Nature communications

Authors' code: PatriarchiLab/InVivoPhotometry (GPL-3.0)

Status: code verified, 39 files readable, 11 matches

Monday, 1 July 2024 (4 papers)

[347] doi:10.1093/genetics/iyae077 [paper, data]

TWISP: a transgenic worm for interrogating signal propagation in Caenorhabditis elegans.

Journal: Genetics

Status: data only, 1 dataset cited

[348] doi:10.1117/1.nph.11.3.035007 [paper, repository]

Optical constraints on two-photon voltage imaging.

Journal: Neurophotonics

Authors' code: luminosmicroscopy.com (no license), adamcohenlab/luminos-microscopy (other)

Status: code verified, 612 files readable, 3 matches

[349] doi:10.1117/1.nph.11.3.034312 [paper, repository]

Computer vision-guided open-source active commutator for neural imaging in freely behaving animals.

Journal: Neurophotonics

Authors' code: bsbrl/Motorized-Commutator (no license)

Status: code verified, 15 files readable, 2 matches

[350] doi:10.1117/1.nph.11.3.035009 [paper]

Two-photon optogenetics-based assessment of neuronal connectivity in healthy and chronic hypoperfusion mice.

Journal: Neurophotonics

Status: code on request

Friday, 28 June 2024 (1 paper)

[351] doi:10.1364/boe.523430 [paper, repository]

3D super-resolution optical fluctuation imaging with temporal focusing two-photon excitation.

Journal: Biomedical optics express

Authors' code: Zenodo 11094685 (CC-BY-4.0)

Status: code verified

Thursday, 27 June 2024 (1 paper)

[352] doi:10.1016/j.celrep.2024.114413 [paper, repository]

Probing multiplexed basal dendritic computations using two-photon 3D holographic uncaging.

Journal: Cell reports

Authors' code: shulanx1/SynMultiplex (no license), shulanx1/stochasticH_python (no license), Zenodo 11304034 (CC-BY-4.0), Zenodo 11303742 (CC-BY-4.0), cortex-lab/KiloSort (GPL-2.0), Zenodo 11303939 (CC-BY-4.0), shulanx1/dynamic_clamp (no license), shulanx1/stochasticHH_python (no license)

Status: code verified, 189 files readable, 4 matches

Wednesday, 19 June 2024 (1 paper)

[353] doi:10.1523/jneurosci.0298-23.2024 [paper]

Cortical Networks Relating to Arousal Are Differentially Coupled to Neural Activity and Hemodynamics.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Status: code on request

Friday, 14 June 2024 (1 paper)

[354] doi:10.1038/s41467-024-49192-2 [paper, repository]

Scanless two-photon voltage imaging.

Journal: Nature communications

Authors' code: Zenodo 11507381 (CC-BY-4.0)

Status: code verified, 1 file readable

Thursday, 13 June 2024 (1 paper)

[355] doi:10.1016/j.cub.2024.05.031 [paper, repository]

Pheromone representation in the ant antennal lobe changes with age.

Journal: Current biology : CB

Authors' code: Zenodo 11151724 (CC-BY-4.0), Zenodo 11151756 (CC-BY-4.0)

Status: code verified, 5 files readable

Monday, 10 June 2024 (1 paper)

[356] doi:10.1098/rstb.2023.0240 [paper, repository]

Enhanced long-term potentiation in the anterior cingulate cortex of tree shrew.

Journal: Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Authors' code: doi:10.6084/m9.figshare.c.7202779 (no license)

Status: code found, still to be checked

Saturday, 8 June 2024 (1 paper)

[357] doi:10.1038/s41598-024-63685-6 [paper, repository]

Disparate nonlinear neural dynamics measured with different techniques in macaque and human V1.

Journal: Scientific reports

Authors' code: jingyang-zhou/vsdDynamics_2024 (no license)

Status: code verified, 6 files readable

Wednesday, 5 June 2024 (1 paper)

[358] doi:10.1016/j.xpro.2024.103110 [paper, repository]

Protocol for calcium imaging and analysis of hippocampal CA1 activity evoked by non-spatial stimuli.

Journal: STAR protocols

Authors' code: Zenodo 11118231 (CC-BY-4.0)

Status: code verified, 19 files readable, 3 matches

Friday, 31 May 2024 (2 papers)

[359] doi:10.1177/0271678x241258576 [paper, repository]

High-resolution vasomotion analysis reveals novel arteriole physiological features and progressive modulation of cerebral vascular networks by stroke.

Journal: Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism

Authors' code: JialabEleven/Vasomotion_analysis (no license)

Status: code verified, 16 files readable, 5 matches

[360] doi:10.1038/s41467-024-48373-3 [paper, repository]

Intrinsic and synaptic determinants of receptive field plasticity in Purkinje cells of the mouse cerebellum.

Journal: Nature communications

Authors' code: tingfenglin-ac/CerebellarPurkinjeRFplasticity (no license), Zenodo 10901777 (CC-BY-4.0)

Status: code verified, 42 files readable, 5 matches

Wednesday, 29 May 2024 (1 paper)

[361] doi:10.7554/elife.94167 [paper, repository]

Pan-cortical 2-photon mesoscopic imaging and neurobehavioral alignment in awake, behaving mice.

Journal: eLife

Authors' code: vickerse1/mesoscope_spontaneous (BSD-3-Clause), sjara/uobrainflex (no license), lindermanlab/ssm (MIT), Zenodo 10966793 (CC-BY-4.0)

Status: code verified, 173 files readable, 9 matches

Tuesday, 28 May 2024 (1 paper)

[362] doi:10.1523/eneuro.0252-23.2024 [paper, repository]

Spatiotemporal Organization of Prefrontal Norepinephrine Influences Neuronal Activity.

Journal: eNeuro

Authors' code: kayelab/nejrgeco (no license)

Status: code verified, 33 files readable, 5 matches

Saturday, 25 May 2024 (1 paper)

[363] doi:10.1016/j.celrep.2024.114244 [paper, repository]

Stimulus information guides the emergence of behavior-related signals in primary somatosensory cortex during learning.

Journal: Cell reports

Authors' code: cortex-lab/suite2p (other), rmaffulli/nit (no license)

Status: code verified, 426 files readable, 6 matches

Thursday, 16 May 2024 (1 paper)

[364] doi:10.1038/s41467-024-48505-9 [paper, repository]

Magnetic voluntary head-fixation in transgenic rats enables lifespan imaging of hippocampal neurons.

Journal: Nature communications

Authors' code: dylan2106/Magnetic-Voluntary-Head-fixation (other), dylan2106/two_photon_collection_cannula (GPL-3.0)

Status: code verified, 50 files readable, 2 matches

Wednesday, 15 May 2024 (3 papers)

[365] doi:10.1523/eneuro.0396-23.2024 [paper, repository]

Topography and Ensemble Activity in the Auditory Cortex of a Mouse Model of Fragile X Syndrome.

Journal: eNeuro

Authors' code: HirtzLab/Imaging_auditory_cortex_fmr1_KO (GPL-3.0)

Status: code verified, 45 files readable, 8 matches

[366] doi:10.7554/elife.91136 [paper, repository]

Functional diversity of dopamine axons in prefrontal cortex during classical conditioning.

Journal: eLife

Authors' code: pharmedku/2024-elife-da-axon (no license)

Status: code verified, 1 file readable

[367] doi:10.7554/elife.95694 [paper, repository]

Comment on 'Accumbens cholinergic interneurons dynamically promote dopamine release and enable motivation'.

Journal: eLife

Authors' code: TritschLab/Taniguchi-Melani-2024 (MIT)

Status: code verified, 120 files readable, 1 match

Tuesday, 14 May 2024 (1 paper)

[368] doi:10.1016/j.isci.2024.109973 [paper]

Functional remodeling of presynaptic voltage-gated calcium channels in superficial layers of the dorsal horn during neuropathic pain.

Journal: iScience

Status: code on request

Thursday, 9 May 2024 (2 papers)

[369] doi:10.1117/1.nph.11.3.033408 [paper]

Encoding of self-initiated actions in axon terminals of the mesocortical pathway.

Journal: Neurophotonics

Status: code on request

[370] doi:10.1016/j.neuron.2024.04.015 [paper, repository]

A latent pool of neurons silenced by sensory-evoked inhibition can be recruited to enhance perception.

Journal: Neuron

Authors' code: llerussell/Naparm (no license)

Status: code verified, 80 files readable, 4 matches

Friday, 3 May 2024 (1 paper)

[371] doi:10.1016/j.celrep.2024.114189 [paper, repository]

Highly local activation of inhibition at the seizure wavefront in vivo.

Journal: Cell reports

Authors' code: Packer-Lab/imagingplus (MIT), Zenodo 10825258 (CC-BY-4.0), Packer-Lab/AllOpticalSeizure (no license), llerussell/Naparm (no license)

Status: code verified, 496 files readable, 19 matches

Wednesday, 1 May 2024 (1 paper)

[372] doi:10.1523/jneurosci.1461-23.2024 [paper, data]

Differential Expression Analysis Identifies Candidate Synaptogenic Molecules for Wiring Direction-Selective Circuits in the Retina.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Status: data only, 1 dataset cited

Tuesday, 30 April 2024 (1 paper)

[373] doi:10.7554/elife.90080 [paper, data]

Aberrant cortical activity, functional connectivity, and neural assembly architecture after photothrombotic stroke in mice.

Journal: eLife

Status: data only, 1 dataset cited

Saturday, 27 April 2024 (1 paper)

[374] doi:10.1016/j.xpro.2024.103027 [paper, data]

Protocol for recording neural activity evoked by electrical stimulation in mice using two-photon calcium imaging.

Journal: STAR protocols

Status: data only, 1 dataset cited

Tuesday, 16 April 2024 (1 paper)

[375] doi:10.1186/s12868-024-00866-z [paper, repository]

Computational modeling of light processing in the habenula and dorsal raphe based on laser ablation of functionally-defined cells.

Journal: BMC neuroscience

Authors' code: nsuhasj/habenulaRaphe (GPL-3.0), figshare 21721058 (CC-BY-4.0)

Status: code verified, 10 files readable, 2 matches

Monday, 15 April 2024 (1 paper)

[376] doi:10.1073/pnas.2303664121 [paper, repository]

Brain-derived neurotrophic factor scales presynaptic calcium transients to modulate excitatory neurotransmission.

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

Authors' code: camilleswang/iGluSnFR-Analysis (GPL-3.0)

Status: empty repository, 2 files readable

Thursday, 11 April 2024 (1 paper)

[377] doi:10.1038/s41422-024-00956-x [paper, repository]

System-level time computation and representation in the suprachiasmatic nucleus revealed by large-scale calcium imaging and machine learning.

Journal: Cell research

Authors' code: RafaWong/SCN-Research-Project (no license)

Status: code verified, 40 files readable, 9 matches

Tuesday, 9 April 2024 (2 papers)

[378] doi:10.7554/elife.89570 [paper, repository]

Neural correlates of perceptual similarity masking in primate V1.

Journal: eLife

Authors' code: Zenodo 10815850 (CC-BY-4.0)

Status: code verified, 9 files readable, 4 matches

[379] doi:10.1364/boe.521478 [paper, repository]

NeuroSeg-III: efficient neuron segmentation in two-photon Ca²⁺ imaging data using self-supervised learning.

Journal: Biomedical optics express

Authors' code: zimo-k/NeuroSeg3 (no license)

Status: code verified, 110 files readable, 6 matches

Saturday, 6 April 2024 (1 paper)

[380] doi:10.1038/s41598-024-58819-9 [paper]

Expression of GCaMP6s in the dentate gyrus induces tonic-clonic seizures.

Journal: Scientific reports

Status: code on request

Thursday, 4 April 2024 (1 paper)

[381] doi:10.1117/1.nph.11.2.024207 [paper]

Blue-shifted genetically encoded Ca&lt;sup&gt;2+&lt;/sup&gt; indicator with enhanced two-photon absorption.

Journal: Neurophotonics

Status: code on request

Wednesday, 3 April 2024 (3 papers)

[382] doi:10.7554/elife.92839 [paper, repository]

Ocular dominance-dependent binocular combination of monocular neuronal responses in macaque V1.

Journal: eLife

Authors' code: supp:PMC10990486/elife-92839-code1.zip (no license)

Status: code verified, 1 file readable

[383] doi:10.1038/s41593-024-01612-8 [paper, repository]

Centripetal integration of past events in hippocampal astrocytes regulated by locus coeruleus.

Journal: Nature neuroscience

Authors' code: PTRRupprecht/Drawing-ROIs-without-GUI (MIT), HelmchenLabSoftware/Centripetal_propagation_astrocytes (GPL-3.0), Zenodo 10420895 (CC-BY-4.0)

Status: code verified, 30 files readable

[384] doi:10.1186/s12974-024-03073-z [paper, repository]

Cranial irradiation disrupts homeostatic microglial dynamic behavior.

Journal: Journal of neuroinflammation

Authors' code: majewska-lab (no license)

Status: code verified

Monday, 1 April 2024 (3 papers)

[385] doi:10.1073/pnas.2315167121 [paper, repository]

Space wandering in the rodent default mode network.

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

Authors' code: tae-nghiem/DMN-space-wandering (no license)

Status: code verified, 3 files readable, 2 matches

[386] doi:10.1117/1.nph.11.2.025003 [paper]

Two-photon imaging of excitatory and inhibitory neural response to infrared neural stimulation.

Journal: Neurophotonics

Status: code on request

[387] doi:10.1117/1.nph.11.2.025005 [paper, repository]

Two-dimensional electro-optical multiphoton microscopy.

Journal: Neurophotonics

Authors' code: kerlin-lab/Farinella_2024 (GPL-2.0)

Status: code verified, 14 files readable, 2 matches

Wednesday, 13 March 2024 (1 paper)

[388] doi:10.1371/journal.pcbi.1011074 [paper, repository]

End-to-end deep learning approach to mouse behavior classification from cortex-wide calcium imaging.

Journal: PLoS computational biology

Authors' code: atakehiro/Neural_Decoding_from_Calcium_Imaging_Data (MIT)

Status: code verified, 17 files readable, 3 matches

Monday, 11 March 2024 (1 paper)

[389] doi:10.1016/j.xpro.2024.102931 [paper, repository]

Protocol for in vivo dual-color fiber photometry in the mouse thalamus.

Journal: STAR protocols

Authors' code: swyeon11/MN-MD (MIT)

Status: code verified, 3 files readable

Friday, 1 March 2024 (1 paper)

[390] doi:10.1038/s41598-024-55608-2 [paper, repository]

Automatic monitoring of neural activity with single-cell resolution in behaving Hydra.

Journal: Scientific reports

Authors' code: raphaelreme/trase-in (MIT), stardist/stardist (BSD-3-Clause)

Status: code verified, 70 files readable, 6 matches

Wednesday, 28 February 2024 (1 paper)

[391] doi:10.1038/s41467-024-46234-7 [paper, repository]

Dendritic mGluR2 and perisomatic Kv3 signaling regulate dendritic computation of mouse starburst amacrine cells.

Journal: Nature communications

Authors' code: ww-uchicago/NC-manuscript-2023 (GPL-3.0)

Status: code verified, 84 files readable, 3 matches

Monday, 26 February 2024 (1 paper)

[392] doi:10.1016/j.xpro.2024.102911 [paper]

Probing cerebellar circuit dysfunction in rodent models of spinocerebellar ataxia by means of in vivo two-photon calcium imaging.

Journal: STAR protocols

Status: code on request

Tuesday, 20 February 2024 (1 paper)

[393] doi:10.1038/s41598-024-54720-7 [paper, repository]

The gephyrin scaffold modulates cortical layer 2/3 pyramidal neuron responsiveness to single whisker stimulation.

Journal: Scientific reports

Authors' code: dcolam/Cluster-Analysis-Plugin (MIT)

Status: code verified, 20 files readable

Thursday, 15 February 2024 (1 paper)

[394] doi:10.1523/eneuro.0352-23.2024 [paper, repository]

A Semi-supervised Pipeline for Accurate Neuron Segmentation with Fewer Ground Truth Labels.

Journal: eNeuro

Authors' code: YijunBao/Shallow-UNet-Neuron-Segmentation_SUNS (GPL-2.0), caseymbaker/SemiSupervisedNeuronSegmentation2p (no license)

Status: code verified, 118 files readable, 10 matches

Saturday, 10 February 2024 (1 paper)

[395] doi:10.1038/s41467-024-45417-6 [paper, repository]

Mesoscopic calcium imaging in a head-unrestrained male non-human primate using a lensless microscope.

Journal: Nature communications

Authors' code: JiminWu/Bio-FlatScopeNHP (no license), Zenodo 10403840 (CC-BY-4.0)

Status: code verified, 118 files readable, 3 matches

Friday, 9 February 2024 (1 paper)

[396] doi:10.1016/j.heliyon.2024.e25910 [paper, repository]

Simultaneous two-photon imaging and wireless EEG recording in mice.

Journal: Heliyon

Authors' code: harnett/Shiqian-analysis (no license), ss276/EEG (no license)

Status: code verified, 46 files readable, 5 matches

Tuesday, 6 February 2024 (1 paper)

[397] doi:10.1117/1.nph.11.s1.s11503 [paper, repository]

Photonic neural probe enabled microendoscopes for light-sheet light-field computational fluorescence brain imaging.

Journal: Neurophotonics

Authors' code: Pding2/Light-field-fiber-bundle-imaging (MIT)

Status: code verified, 25 files readable, 1 match

Thursday, 1 February 2024 (1 paper)

[398] doi:10.1093/brain/awad358 [paper, data]

Microglia sense astrocyte dysfunction and prevent disease progression in an Alexander disease model.

Journal: Brain : a journal of neurology

Status: data only, 1 dataset cited

Thursday, 25 January 2024 (1 paper)

[399] doi:10.1117/1.nph.11.2.024202 [paper, repository]

Seizure event detection using intravital two-photon calcium imaging data.

Journal: Neurophotonics

Authors' code: Stern-MA/2PCISz_RecDetect (GPL-3.0)

Status: code verified, 16 files readable, 10 matches

Wednesday, 24 January 2024 (2 papers)

[400] doi:10.1117/1.jbo.29.1.016501 [paper]

Rapid, high-contrast, and steady volumetric imaging with Bessel-beam-based two-photon fluorescence microscopy.

Journal: Journal of biomedical optics

Status: code on request

[401] doi:10.1093/pnasnexus/pgae032 [paper, data]

Unraveling the hierarchical structure of posture and muscle activity changes during mating of <i>Caenorhabditis elegans</i>.

Journal: PNAS nexus

Status: data only, 1 dataset cited

Thursday, 18 January 2024 (1 paper)

[402] doi:10.1093/braincomms/fcae013 [paper, repository]

&lt;i&gt;In vivo&lt;/i&gt; calcium imaging shows that satellite glial cells have increased activity in painful states.

Journal: Brain communications

Authors' code: OSF jg5zr (no license)

Status: empty repository

Wednesday, 17 January 2024 (1 paper)

[403] doi:10.1117/1.nph.11.3.033402 [paper]

Imaging different cell populations in the mouse olfactory bulb using the genetically encoded voltage indicator ArcLight.

Journal: Neurophotonics

Status: code on request

Tuesday, 16 January 2024 (1 paper)

[404] doi:10.1364/boe.510512 [paper]

Impact of a tilted coverslip on two-photon and STED microscopy.

Journal: Biomedical optics express

Status: code on request

Thursday, 11 January 2024 (2 papers)

[405] doi:10.1523/eneuro.0315-23.2023 [paper]

Striatal Neurons Are Recruited Dynamically into Collective Representations of Self-Initiated and Learned Actions in Freely Moving Mice.

Journal: eNeuro

Status: code on request

[406] doi:10.1038/s41593-023-01545-8 [paper, data]

Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses.

Journal: Nature neuroscience

Status: data only, 1 dataset cited

Friday, 5 January 2024 (1 paper)

[407] doi:10.1016/j.crmeth.2023.100681 [paper, repository]

A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets.

Journal: Cell reports methods

Authors' code: Zenodo 10210141 (BSD-3-Clause), Zenodo 10198748 (GPL-3.0), gin.g-node.org/inm-6/cobrawap_publication_code (BSD-3-Clause), Zenodo 17197618 (GPL-3.0), Zenodo 17048329 (GPL-3.0), Zenodo 15005123 (GPL-3.0), Zenodo 13134351 (GPL-3.0), Zenodo 13268635 (GPL-3.0), Zenodo 13268634 (GPL-3.0)

Status: code verified, 562 files readable, 16 matches

Wednesday, 3 January 2024 (2 papers)

[408] doi:10.1038/s41467-023-44363-z [paper, repository]

Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization.

Journal: Nature communications

Authors' code: allensdk.readthedocs.io (no license), hadivafaii/Ca-fMRI (no license), premgopalan/svinet (GPL-3.0), AllenInstitute/mouse_connectivity_models (BSD-2-Clause), santofortunato.net/resources (no license), juhuntenburg/mouse_gradients (no license), bioimagesuiteweb.github.io/webapp (no license), CoBrALab/RABIES (other), YaleMRRC/calPrep (no license)

Status: code verified, 270 files readable, 7 matches

[409] doi:10.1364/boe.507517 [paper, repository]

Numerical study of a convective cooling strategy for increasing safe power levels in two-photon brain imaging.

Journal: Biomedical optics express

Authors' code: adi-roy/2pPointScanHeating (no license)

Status: code verified, 18 files readable, 3 matches

Monday, 1 January 2024 (4 papers)

[410] doi:10.1117/1.nph.11.1.015006 [paper, repository]

Contribution of optical resolution to the spatial precision of two-photon optogenetic photostimulation <i>in vivo</i>.

Journal: Neurophotonics

Authors' code: Packer-Lab/OPSF_vs_PPSF (no license)

Status: code verified, 4 files readable, 4 matches

[411] doi:10.1117/1.nph.11.1.014413 [paper]

Model-based correction of rapid thermal confounds in fluorescence neuroimaging of targeted perturbation.

Journal: Neurophotonics

Status: code on request

[412] doi:10.1117/1.nph.11.1.014305 [paper, repository]

FiPhA: an open-source platform for fiber photometry analysis.

Journal: Neurophotonics

Authors' code: mfbridge/FiPhA (MIT)

Status: code verified, 45 files readable, 10 matches

[413] doi:10.1117/1.nph.11.1.014306 [paper, repository]

Low-cost reversible tandem lens mesoscope for brain imaging in rodents.

Journal: Neurophotonics

Authors' code: juliettecheyne/cheyne_lab (no license)

Status: code verified, 114 files readable, 1 match

Friday, 22 December 2023 (2 papers)

[414] doi:10.7554/elife.86749 [paper, data]

Imaging microglia surveillance during sleep-wake cycles in freely behaving mice.

Journal: eLife

Status: data only, 1 dataset cited

[415] doi:10.1117/1.jbo.28.12.126006 [paper, repository]

Restoration of metabolic functional metrics from label-free, two-photon human tissue images using multiscale deep-learning-based denoising algorithms.

Journal: Journal of biomedical optics

Authors' code: CSBDeep/CSBDeep (BSD-3-Clause), Tufts-University/Denoising2PImages (MIT)

Status: code verified, 80 files readable, 4 matches

Thursday, 21 December 2023 (1 paper)

[416] doi:10.1038/s41592-023-02098-1 [paper, data]

The Cousa objective: a long-working distance air objective for multiphoton imaging in vivo.

Journal: Nature methods

Status: data only, 1 dataset cited

Monday, 18 December 2023 (1 paper)

[417] doi:10.1523/eneuro.0096-23.2023 [paper, repository]

Meso-Py: Dual Brain Cortical Calcium Imaging in Mice during Head-Fixed Social Stimulus Presentation.

Journal: eNeuro

Authors' code: ubcbraincircuits/dual-mouse (no license)

Status: code verified, 331 files readable, 11 matches

Friday, 15 December 2023 (1 paper)

[418] doi:10.1097/j.pain.0000000000003116 [paper, repository]

Assessing spontaneous sensory neuron activity using in vivo calcium imaging.

Journal: Pain

Authors' code: sonialouise/ts_class (no license)

Status: code verified, 8 files readable

Friday, 8 December 2023 (1 paper)

[419] doi:10.1038/s41467-023-43920-w [paper, repository]

Norepinephrine regulates calcium signals and fate of oligodendrocyte precursor cells in the mouse cerebral cortex.

Journal: Nature communications

Authors' code: ars.els-cdn.com/content/image (no license)

Status: code verified

Thursday, 7 December 2023 (1 paper)

[420] doi:10.7554/elife.89682 [paper, repository]

Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines.

Journal: eLife

Authors' code: Zenodo 10278270 (CC-BY-4.0)

Status: empty repository

Saturday, 2 December 2023 (1 paper)

[421] doi:10.1016/j.xpro.2023.102760 [paper, repository]

Protocol to image and analyze hippocampal network dynamics in non-anesthetized mouse pups.

Journal: STAR protocols

Authors' code: cossartlab/motion-correction (no license), Zenodo 10041302 (CC-BY-4.0), Zenodo 10041434 (CC-BY-4.0)

Status: code verified, 3 files readable

Friday, 1 December 2023 (1 paper)

[422] doi:10.1016/j.isci.2023.108603 [paper]

Hippocampal cognitive and relational map paradigms explored by multisensory encoding recording with wide-field calcium imaging.

Journal: iScience

Status: code on request

Monday, 27 November 2023 (1 paper)

[423] doi:10.1038/s41467-023-43254-7 [paper, repository]

Cortical reactivation of spatial and non-spatial features coordinates with hippocampus to form a memory dialogue.

Journal: Nature communications

Authors' code: LelouchLamperougeVI/OfflineEnsembles (GPL-3.0), Zenodo 10030861 (CC-BY-4.0)

Status: code verified, 24 files readable, 2 matches

Wednesday, 22 November 2023 (1 paper)

[424] doi:10.1523/jneurosci.0353-23.2023 [paper]

Prostaglandin E₂ Induces Long-Lasting Inhibition of Noradrenergic Neurons in the Locus Coeruleus and Moderates the Behavioral Response to Stressors.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Status: code on request

Wednesday, 15 November 2023 (1 paper)

[425] doi:10.1007/s00424-023-02871-3 [paper, repository]

Amyloid plaques and normal ageing have differential effects on microglial Ca&lt;sup&gt;2+&lt;/sup&gt; activity in the mouse brain.

Journal: Pflugers Archiv : European journal of physiology

Authors' code: AttwellLab/Microglia (MIT), AttwellLab/MyelinCalcium (MIT), AttwellLab (no license)

Status: code verified, 16 files readable, 2 matches

Friday, 3 November 2023 (1 paper)

[426] doi:10.1016/j.molmet.2023.101833 [paper, repository]

AgRP neuron activity promotes associations between sensory and nutritive signals to guide flavor preference.

Journal: Molecular metabolism

Authors' code: nathanielnyema/fnc_agrp_project (no license), nathanielnyema/lickometer (no license)

Status: code verified, 13 files readable, 8 matches

Thursday, 2 November 2023 (1 paper)

[427] doi:10.1038/s41467-023-42777-3 [paper, repository]

Striatum-projecting prefrontal cortex neurons support working memory maintenance.

Journal: Nature communications

Authors' code: HelmchenLabSoftware/wilhelm-sych-tmaze-analysis (no license)

Status: code verified, 118 files readable, 7 matches

Tuesday, 31 October 2023 (1 paper)