{
  "publications": [
    {
      "id": "olfactory-cortex-satiation-2025",
      "first_author": "Lo",
      "title": "Feeding-induced olfactory cortex suppression reduces satiation",
      "journal": "Neuron",
      "year": 2025,
      "url": "https://doi.org/10.1016/j.neuron.2025.07.020",
      "doi": "10.1016/j.neuron.2025.07.020",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Schmitz", "Johenning"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "Charité – Universitätsmedizin Berlin",
      "external_institution": "Charité – Universitätsmedizin Berlin / DZNE Berlin",
      "notes": "Schmitz & Johenning labs; remote support with BakingTray/StitchIt"
    },
    {
      "id": "entorhinal-l3-rabies-2025",
      "first_author": "Chen",
      "title": "Direct Hippocampal and Thalamic Inputs to Layer 3 Pyramidal Cells in the Medial Entorhinal Cortex Revealed by Monosynaptic Rabies Tracing",
      "journal": "Neuroscience Bulletin",
      "year": 2025,
      "url": "https://doi.org/10.1007/s12264-025-01363-x",
      "doi": "10.1007/s12264-025-01363-x",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Schmitz"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "Charité – Universitätsmedizin Berlin",
      "external_institution": "Charité – Universitätsmedizin Berlin / DZNE Berlin",
      "notes": "Schmitz labs; remote support with BakingTray/StitchIt"
    },
    {
      "id": "bakingtray-brainsaw-2026",
      "first_author": "Campbell",
      "title": "High-throughput serial two-photon tomography with BakingTray and BrainSaw",
      "journal": "bioRxiv",
      "year": 2026,
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.28.748989v1",
      "doi": "10.64898/2026.09.28.748989",
      "amf_authorship": "first",
      "affiliation": "swc",
      "pi": [],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "zapit-2026",
      "first_author": "Lohse",
      "title": "Zapit: Open Source Laser-Scanning Photostimulation For Neuroscience",
      "journal": "eLife (reviewed preprint)",
      "year": 2026,
      "url": "https://elifesciences.org/reviewed-preprints/111872",
      "doi": "10.7554/eLife.111872.1",
      "amf_authorship": "first",
      "affiliation": "swc",
      "pi": [],
      "platforms": ["Technical services"],
      "equipment": [],
      "software_tools": ["Zapit"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "std-measurements-2025",
      "first_author": "Lees",
      "title": "Standardised Measurements for Monitoring and Comparing Multiphoton Microscope Systems",
      "journal": "Nature Protocols",
      "year": 2025,
      "url": "https://www.nature.com/articles/s41596-024-01120-w",
      "doi": "10.1038/s41596-024-01120-w",
      "amf_authorship": "first",
      "affiliation": "swc",
      "pi": [],
      "platforms": ["Technical services"],
      "equipment": [],
      "software_tools": ["MPQC"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "blackcap-atlas-2026",
      "first_author": "Sirmpilatze",
      "title": "An open-source three-dimensional digital brain atlas of a migratory bird, the Eurasian blackcap",
      "journal": "Current Biology",
      "year": 2026,
      "url": "https://www.cell.com/current-biology/fulltext/S0960-9822(26)00323-4",
      "doi": "10.1016/j.cub.2026.03.034",
      "amf_authorship": "middle",
      "affiliation": "swc",
      "pi": ["Weiler"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "ibl-reproducibility-2025",
      "first_author": "International Brain Laboratory",
      "title": "Reproducibility of in-vivo electrophysiological measurements in mice",
      "journal": "eLife",
      "year": 2025,
      "url": "https://elifesciences.org/reviewed-preprints/100840",
      "doi": "10.7554/eLife.100840",
      "amf_authorship": "middle",
      "affiliation": "swc",
      "pi": [],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt","Lasagna"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "International Brain Laboratory (IBL)",
      "notes": "Collaboration with IBL"
    },
    {
      "id": "insihgt-2024",
      "first_author": "Yau",
      "title": "INSIHGT: An accessible multi-scale, multi-modal 3D spatial biology platform",
      "journal": "Nature Communications",
      "year": 2024,
      "url": "https://www.nature.com/articles/s41467-024-55248-0",
      "doi": "10.1038/s41467-024-55248-0",
      "amf_authorship": "middle",
      "affiliation": "external",
      "pi": [],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["MesoSPIM"],
      "software_tools": [],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "Chinese University of Hong Kong",
      "notes": "In collaboration with colleagues at The Chinese University of Hong Kong"
    },
    {
      "id": "cosmic-kidney-2024",
      "first_author": "Siew",
      "title": "Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction",
      "journal": "Nature Communications",
      "year": 2024,
      "url": "https://www.nature.com/articles/s41467-024-49212-1",
      "doi": "10.1038/s41467-024-49212-1",
      "amf_authorship": "middle",
      "affiliation": "external",
      "pi": ["Siew", "Walsh"],
      "platforms": ["Histology", "Whole-brain imaging"],
      "equipment": ["MesoSPIM"],
      "software_tools": [],
      "techniques": ["RNAscope"],
      "instrument_location": "AMF",
      "external_institution": "UCL Department of Renal Medicine",
      "notes": "In collaboration with Siew & Walsh, Department of Renal Medicine, UCL"
    },
    {
      "id": "antibody-stabilization-2022",
      "first_author": "Lai",
      "title": "Antibody stabilization for thermally accelerated deep immunostaining",
      "journal": "Nature Methods",
      "year": 2022,
      "url": "https://www.nature.com/articles/s41592-022-01569-1",
      "doi": "10.1038/s41592-022-01569-1",
      "amf_authorship": "middle",
      "affiliation": "external",
      "pi": [],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw", "MesoSPIM"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "Chinese University of Hong Kong",
      "notes": "In collaboration with colleagues at The Chinese University of Hong Kong"
    },
    {
      "id": "mesospim-initiative-2019",
      "first_author": "Voigt",
      "title": "The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue",
      "journal": "Nature Methods",
      "year": 2019,
      "url": "https://www.nature.com/articles/s41592-019-0554-0",
      "doi": "10.1038/s41592-019-0554-0",
      "amf_authorship": "middle",
      "affiliation": "external",
      "pi": [],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["MesoSPIM"],
      "software_tools": [],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": "Methods paper"
    },
    {
      "id": "replay-procedural-memory-2026",
      "first_author": "Thompson",
      "title": "Replay of procedural memory is independent of the hippocampus",
      "journal": "Nature Neuroscience",
      "year": 2026,
      "url": "https://www.nature.com/articles/s41593-026-02362-5",
      "doi": "10.1038/s41593-026-02362-5",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Stephenson-Jones"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["AxioScan", "BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": ["IHC"],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "brain-wide-map-2025",
      "first_author": "International Brain Laboratory",
      "title": "A Brain-Wide Map of Neural Activity during Complex Behaviour",
      "journal": "Nature",
      "year": 2025,
      "url": "https://pubmed.ncbi.nlm.nih.gov/40903598",
      "doi": "10.1038/s41586-025-09235-0",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": [],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt","Lasagna"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "International Brain Laboratory (IBL)",
      "notes": "SWC and IBL"
    },
    {
      "id": "dopaminergic-teaching-signal-2025",
      "first_author": "Greenstreet",
      "title": "Dopaminergic action prediction errors serve as a value-free teaching signal",
      "journal": "Nature",
      "year": 2025,
      "url": "https://www.nature.com/articles/s41586-025-09008-9",
      "doi": "10.1038/s41586-025-09008-9",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Stephenson-Jones", "Clopath", "Margrie"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw", "AxioScan"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": ["IHC"],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "layer6-corticocortical-2025",
      "first_author": "Weiler",
      "title": "Layer 6 corticocortical neurons are a major route for intra and interhemispheric feedback",
      "journal": "eLife",
      "year": 2025,
      "url": "https://elifesciences.org/articles/100478",
      "doi": "10.7554/eLife.100478",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Margrie"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw", "Leica SP8"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "subcortical-switchboard-2025",
      "first_author": "Ahmadlou",
      "title": "A subcortical switchboard for perseverative, exploratory and disengaged states",
      "journal": "Nature",
      "year": 2025,
      "url": "https://www.nature.com/articles/s41586-025-08672-1",
      "doi": "10.1038/s41586-025-08672-1",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Hofer"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw", "Leica SP8"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "hamfish-medial-amygdala-2025",
      "first_author": "Edwards",
      "title": "Combined transcriptomic, connectivity, and activity profiling of the medial amygdala using highly amplified multiplexed in situ hybridization (hamFISH)",
      "journal": "eLife (reviewed preprint)",
      "year": 2025,
      "url": "https://elifesciences.org/reviewed-preprints/105388",
      "doi": "10.7554/eLife.105388.2",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Isogai"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "motor-vestibular-signals-2025",
      "first_author": "Vélez-Fort",
      "title": "Motor and vestibular signals in the visual cortex permit the separation of self versus externally generated visual motion",
      "journal": "Cell",
      "year": 2025,
      "url": "https://www.cell.com/cell/fulltext/S0092-8674(25)00101-1",
      "doi": "10.1016/j.cell.2025.01.032",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Clopath", "Margrie"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "overwriting-an-instinct-2025",
      "first_author": "Mederos",
      "title": "Overwriting an instinct: Visual cortex instructs learning to suppress fear responses",
      "journal": "Science",
      "year": 2025,
      "url": "https://www.science.org/doi/10.1126/science.adr2247",
      "doi": "10.1126/science.adr2247",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Hofer"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": ["RNAscope"],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "tacto-visual-integration-2024",
      "first_author": "Weiler",
      "title": "A primary sensory cortical interareal feedforward inhibitory circuit for tacto-visual integration",
      "journal": "Nature Communications",
      "year": 2024,
      "url": "https://www.nature.com/articles/s41467-024-47459-2",
      "doi": "10.1038/s41467-024-47459-2",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Margrie", "Teichert"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw", "Leica SP8"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "cortico-collicular-circuit-2023",
      "first_author": "Campagner",
      "title": "A cortico-collicular circuit for orienting to shelter during escape",
      "journal": "Nature",
      "year": 2023,
      "url": "https://www.nature.com/articles/s41586-022-05553-9",
      "doi": "10.1038/s41586-022-05553-9",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Margrie", "Branco"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "aav-endothelial-tropism-2023",
      "first_author": "Chen",
      "title": "Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates",
      "journal": "Nature Communications",
      "year": 2023,
      "url": "https://www.nature.com/articles/s41467-023-38582-7",
      "doi": "10.1038/s41467-023-38582-7",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Akrami"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": "Akrami lab plus external collaborators"
    },
    {
      "id": "cortical-feedback-loops-2022",
      "first_author": "Voitov",
      "title": "Cortical feedback loops bind distributed representations of working memory",
      "journal": "Nature",
      "year": 2022,
      "url": "https://www.nature.com/articles/s41586-022-05014-3",
      "doi": "10.1038/s41586-022-05014-3",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Mrsic-Flogel"],
      "platforms": ["Technical services"],
      "equipment": ["MesoScope"],
      "software_tools": [],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": "AMF provided assistance with multi-photon microscopy"
    },
    {
      "id": "ethological-events-amygdala-2022",
      "first_author": "Mazuski",
      "title": "Representation of ethological events by basolateral amygdala neurons",
      "journal": "Cell Reports",
      "year": 2022,
      "url": "https://www.sciencedirect.com/science/article/pii/S2211124722006982",
      "doi": "10.1016/j.celrep.2022.110921",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["O'Keefe"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw", "AxioScan"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "independent-response-modulation-2022",
      "first_author": "Kanamori",
      "title": "Independent response modulation of visual cortical neurons by attentional and behavioral states",
      "journal": "Neuron",
      "year": 2022,
      "url": "https://www.cell.com/neuron/fulltext/S0896-6273(22)00803-0#secsectitle0065",
      "doi": "10.1016/j.neuron.2022.08.028",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Mrsic-Flogel"],
      "platforms": ["Histology", "Technical services"],
      "equipment": ["MesoScope"],
      "software_tools": [],
      "techniques": ["RNAscope"],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": "Histology (RNAscope) and multi-photon assistance"
    },
    {
      "id": "marker-location-determination-2022",
      "first_author": "Tyson",
      "title": "Accurate determination of marker location within whole-brain microscopy images",
      "journal": "Scientific Reports",
      "year": 2022,
      "url": "https://doi.org/10.1038/s41598-021-04676-9",
      "doi": "10.1038/s41598-021-04676-9",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Margrie"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "deep-learning-3d-cell-detection-2021",
      "first_author": "Tyson",
      "title": "A deep learning algorithm for 3D cell detection in whole mouse brain image datasets",
      "journal": "PLOS Computational Biology",
      "year": 2021,
      "url": "https://doi.org/10.1371/journal.pcbi.1009074",
      "doi": "10.1371/journal.pcbi.1009074",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Margrie"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw", "TissueCyte"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "retrosplenial-cortex-2021",
      "first_author": "Keshavarzi",
      "title": "The retrosplenial cortex combines internal and external cues to encode head velocity during navigation",
      "journal": "Neuron",
      "year": 2021,
      "url": "http://dx.doi.org/10.1016/j.neuron.2021.10.031",
      "doi": "10.1016/j.neuron.2021.10.031",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Margrie"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw", "Imager"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "flexible-inhibitory-control-2021",
      "first_author": "Fratzl",
      "title": "Flexible inhibitory control of visually-evoked defensive behavior by the ventral lateral geniculate nucleus",
      "journal": "Neuron",
      "year": 2021,
      "url": "https://www.sciencedirect.com/science/article/pii/S0896627321006577",
      "doi": "10.1016/j.neuron.2021.09.003",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Hofer", "Branco"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["BrainSaw", "Leica SP8"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "intracortical-transthalamic-pathways-2021",
      "first_author": "Blot",
      "title": "Visual intracortical and transthalamic pathways carry distinct information to cortical areas",
      "journal": "Neuron",
      "year": 2021,
      "url": "https://www.sciencedirect.com/science/article/pii/S089662732100283X?via%3Dihub",
      "doi": "10.1016/j.neuron.2021.04.017",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Hofer"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["Leica SP8", "BrainSaw", "AxioScan"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "mesoscale-cortical-dynamics-2021",
      "first_author": "Orsolic",
      "title": "Mesoscale cortical dynamics reflect the interaction of sensory evidence and temporal expectation during perceptual decision-making",
      "journal": "Neuron",
      "year": 2021,
      "url": "https://www.sciencedirect.com/science/article/pii/S0896627321002014?via%3Dihub",
      "doi": "10.1016/j.neuron.2021.03.031",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Mrsic-Flogel"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "University of Zurich",
      "notes": ""
    },
    {
      "id": "l6-head-visual-motion-2018",
      "first_author": "Vélez-Fort",
      "title": "A Circuit for Integration of Head- and Visual-Motion Signals in Layer 6 of Mouse Primary Visual Cortex",
      "journal": "Neuron",
      "year": 2018,
      "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896233/",
      "doi": "10.1016/j.neuron.2018.02.023",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Margrie"],
      "platforms": ["Whole-brain imaging", "Histology"],
      "equipment": ["Leica SP8", "TissueCyte"],
      "software_tools": [],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    },
    {
      "id": "single-cell-projections-visual-cortex-2018",
      "first_author": "Han",
      "title": "The logic of single-cell projections from visual cortex",
      "journal": "Nature",
      "year": 2018,
      "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6585423/",
      "doi": "10.1038/nature26159",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": [],
      "platforms": [],
      "equipment": ["TissueCyte"],
      "software_tools": ["MaSIV","StitchIt", "ARAtools", "Lasagna"],
      "techniques": [],
      "instrument_location": "Biozentrum, University of Basel",
      "external_institution": "Biozentrum, University of Basel",
      "notes": ""
    },
    {
      "id": "barcoded-rabies-connectomics-2025",
      "first_author": "Becalick",
      "title": "Barcoded Rabies In Situ Connectomics for high-throughput reconstruction of neural circuits",
      "journal": "bioRxiv",
      "year": 2025,
      "url": "https://www.biorxiv.org/content/10.1101/2025.07.16.665048v1.full",
      "doi": "10.1101/2025.07.16.665048",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": [],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "Francis Crick Institute",
      "external_institution": "Francis Crick Institute",
      "notes": ""
    },
    {
      "id": "deep-learning-cell-types-2025",
      "first_author": "Beau",
      "title": "A deep-learning strategy to identify cell types across species from high-density extracellular recordings",
      "journal": "Cell",
      "year": 2025,
      "url": "https://www.cell.com/cell/abstract/S0092-8674(25)00110-2",
      "doi": "10.1016/j.cell.2025.01.041",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": [],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "UCL, Clark",
      "external_institution": "UCL",
      "notes": ""
    },
    {
      "id": "sound-evoked-visual-cortex-2023",
      "first_author": "Bimbard",
      "title": "Behavioral origin of sound-evoked activity in mouse visual cortex",
      "journal": "Nature Neuroscience",
      "year": 2023,
      "url": "https://www.nature.com/articles/s41593-022-01227-x",
      "doi": "10.1038/s41593-022-01227-x",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Harris", "Carandini"],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "UCL, Clark",
      "external_institution": "UCL",
      "notes": ""
    },
    {
      "id": "rabies-connectivity-tracing-2023",
      "first_author": "Tran-Van-Minh",
      "title": "Quantitative analysis of rabies virus-based synaptic connectivity tracing",
      "journal": "PLOS ONE",
      "year": 2023,
      "url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0278053#sec016",
      "doi": "10.1371/journal.pone.0278053",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Rancz"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "Francis Crick Institute",
      "notes": "Ede Rancz's Lab"
    },
    {
      "id": "automated-home-cage-2023",
      "first_author": "Ho",
      "title": "A fully automated home cage for long-term continuous phenotyping of mouse cognition and behavior",
      "journal": "Cell Reports Methods",
      "year": 2023,
      "url": "https://www.sciencedirect.com/science/article/pii/S2667237523001686?via%3Dihub#appsec2",
      "doi": "10.1016/j.crmeth.2023.100532",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Krupic"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "University of Cambridge",
      "notes": "Julija Krupic and colleagues used BrainSaw at the AMF"
    },
    {
      "id": "excitation-inhibition-changes-2022",
      "first_author": "Esmaeili",
      "title": "Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas",
      "journal": "PLoS Biology",
      "year": 2022,
      "url": "https://doi.org/10.1371/journal.pbio.3001667",
      "doi": "10.1371/journal.pbio.3001667",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Petersen"],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "EPFL",
      "external_institution": "EPFL",
      "notes": "Carl Petersen's Lab"
    },
    {
      "id": "l23-barrel-cortex-morphology-2022",
      "first_author": "Liu",
      "title": "Axonal and Dendritic Morphology of Excitatory Neurons in Layer 2/3 Mouse Barrel Cortex Imaged Through Whole-Brain Two-Photon Tomography and Registered to a Digital Brain Atlas",
      "journal": "Frontiers in Neuroanatomy",
      "year": 2022,
      "url": "https://doi.org/10.3389/fnana.2021.791015",
      "doi": "10.3389/fnana.2021.791015",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Petersen"],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "EPFL",
      "external_institution": "EPFL",
      "notes": "Carl Petersen's Lab"
    },
    {
      "id": "dendritic-domain-sampling-2022",
      "first_author": "Galloni",
      "title": "Dendritic Domain-Specific Sampling of Long-Range Axons Shapes Feedforward and Feedback Connectivity of L5 Neurons",
      "journal": "Journal of Neuroscience",
      "year": 2022,
      "url": "https://pubmed.ncbi.nlm.nih.gov/35241493/",
      "doi": "10.1523/JNEUROSCI.1620-21.2022",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Rancz"],
      "platforms": ["Whole-brain imaging"],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": "Francis Crick Institute",
      "notes": "Ede Rancz's Lab"
    },
    {
      "id": "salmonella-persistence-2021",
      "first_author": "Li",
      "title": "Tissue compartmentalization enables Salmonella persistence during chemotherapy",
      "journal": "PNAS",
      "year": 2021,
      "url": "https://pubmed.ncbi.nlm.nih.gov/34911764/",
      "doi": "10.1073/pnas.2113951118",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": [],
      "platforms": [],
      "equipment": ["TissueCyte"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "Biozentrum, University of Basel",
      "external_institution": "Biozentrum, University of Basel",
      "notes": ""
    },
    {
      "id": "rapid-suppression-sensory-motor-2021",
      "first_author": "Esmaeili",
      "title": "Rapid suppression and sustained activation of distinct cortical regions for a delayed sensory-triggered motor response",
      "journal": "Neuron",
      "year": 2021,
      "url": "https://www.cell.com/neuron/fulltext/S0896-6273(21)00331-7",
      "doi": "10.1016/j.neuron.2021.05.005",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Petersen"],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "EPFL",
      "external_institution": "EPFL",
      "notes": "Carl Petersen's Lab"
    },
    {
      "id": "thalamocortical-inputs-whisker-2020",
      "first_author": "El-Boustani",
      "title": "Anatomically and functionally distinct thalamocortical inputs to primary and secondary mouse whisker somatosensory cortices",
      "journal": "Nature Communications",
      "year": 2020,
      "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335197/",
      "doi": "10.1038/s41467-020-17087-7",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Petersen"],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "EPFL",
      "external_institution": "EPFL",
      "notes": "Carl Petersen's Lab"
    },
    {
      "id": "whisker-tongue-jaw-sensorimotor-2019",
      "first_author": "Mayrhofer",
      "title": "Distinct Contributions of Whisker Sensory Cortex and Tongue-Jaw Motor Cortex in a Goal-Directed Sensorimotor Transformation",
      "journal": "Neuron",
      "year": 2019,
      "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859494/",
      "doi": "10.1016/j.neuron.2019.07.008",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Petersen"],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt"],
      "techniques": [],
      "instrument_location": "EPFL",
      "external_institution": "EPFL",
      "notes": "Carl Petersen's Lab"
    },
    {
      "id": "chromatically-correct-2023",
      "first_author": "Blanc",
      "title": "Chromatically Corrected Multicolor Multiphoton Microscopy",
      "journal": "ACS Photonics",
      "year": 2023,
      "url": "https://pubs.acs.org/apchd5/article/10/12/4104/336569/Chromatically-Corrected-Multicolor-Multiphoton",
      "doi": "doi.org/10.1021/acsphotonics.3c01104",
      "amf_authorship": "none",
      "affiliation": "external",
      "pi": ["Beaurepaire"],
      "platforms": [],
      "equipment": ["BrainSaw"],
      "software_tools": ["BakingTray","StitchIt","MPQC"],
      "techniques": [],
      "instrument_location": "Ecole Polytechnique",
      "external_institution": "Ecole Polytechnique",
      "notes": "Emmanuel Beaurepaire's lab"
    },
    {
      "id": "frontal-motor-economic-decisions-2026",
      "first_author": "Gauld",
      "title": "A frontal motor circuit for economic decisions and actions",
      "journal": "bioRxiv",
      "year": 2026,
      "url": "https://www.biorxiv.org/content/10.64898/2025.12.11.693624v2.full",
      "doi": "10.64898/2025.12.11.693624",
      "amf_authorship": "none",
      "affiliation": "swc",
      "pi": ["Erlich","Duan"],
      "platforms": ["Technical services"],
      "equipment": [],
      "software_tools": ["Zapit"],
      "techniques": [],
      "instrument_location": "AMF",
      "external_institution": null,
      "notes": ""
    }
  ]
}