Publications

AMF Publications

• Zapit: Open Source Random-Access Photostimulation For Neuroscience; bioRxiv 2024
• Standardised Measurements for Monitoring and Comparing Multiphoton Microscope Systems; bioRxiv 2024

AMF Collaborative Work

• Reproducibility of in-vivo electrophysiological measurements in mice; bioRxiv 2023, in collaboration with IBL, BrainSaw
• Antibody stabilization for thermally accelerated deep immunostaining; Nature Methods 2022, BrainSaw, MesoSPIM
• The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue; Nature Methods 2019

Publications From SWC Groups Using The Facility

• A cortico-collicular circuit for orienting to shelter during escape; Nature 2023, Margrie and Branco, BrainSaw
• A subcortical switchboard for exploratory, exploitatory, and disengaged states; bioRxiv 2022, Hofer, BrainSaw
• A Brain-Wide Map of Neural Activity during Complex Behaviour; bioRxiv 2023, SWC and IBL, BrainSaw
• Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates; Nature Communications 2023, Akrami + external collaborators, BrainSaw
• A primary sensory cortical interareal feedforward inhibitory circuit for tacto-visual integration; bioRxiv 2022, Margrie, BrainSaw
• Representation of ethological events by basolateral amygdala neurons; Cell Reports 2022, O’Keefe, BrainSaw
• Independent response modulation of visual cortical neurons by attentional and behavioral states; Neuron 2022, Mrsic-Flogel, Histology (RNAscope) and multi-photon assistance
• Accurate determination of marker location within whole-brain microscopy images; Scientific Reports 2022, Margrie, BrainSaw
• A deep learning algorithm for 3D cell detection in whole mouse brain image datasets; PLOS Comp Bio 2021, Margrie, BrainSaw, TissueVision
• The retrosplenial cortex combines internal and external cues to encode head velocity during navigation; Neuron 2021, Margrie, BrainsSaw
• Flexible inhibitory control of visually-evoked defensive behavior by the ventral lateral geniculate nucleus; Neuron 2021, Hofer and Branco, BrainsSaw
• Excitatory and inhibitory L2/3 neurons in mouse primary visual cortex are balanced in their input connectivity; bioRxiv 2020, Margrie, TissueVision
• Visual intracortical and transthalamic pathways carry distinct information to cortical areas; Neuron 2021, Hofer, SP8, BrainSaw
• Mesoscale cortical dynamics reflect the interaction of sensory evidence and temporal expectation during perceptual decision-making; Neuron 2021, Mrsic-Flogel, BrainSaw
• A Circuit for Integration of Head- and Visual-Motion Signals in Layer 6 of Mouse Primary Visual Cortex; Neuron 2018, Margrie, Leica SP8, TissueVision
• The logic of single-cell projections from visual cortex; Nature 2018, StitchIt, ARA_tools, Lasagna

Publications From SWC Groups Acknowledging The Facility

• Cortical feedback loops bind distributed representations of working memory; Nature 2022, Mrsic-Flogel, multi-photon assistance

Publications From External Groups Using Our Tools

• An adaptable, reusable, and light implant for chronic Neuropixels probes; bioRxiv 2024, BrainSaw and StitchIt
• A deep-learning strategy to identify cell types across species from high-density extracellular recordings; bioRxiv 2024, BrainSaw system built at UCL.
• Behavioral origin of sound-evoked activity in mouse visual cortex; Nature Neuroscience 2023, from Harris and Carandini, BrainSaw and StitchIt
• Quantitative analysis of rabies virus-based synaptic connectivity tracing; PLOS ONE 2023, from Ede Rancz’s Lab, BrainSaw and StitichIt
• A fully automated home cage for long-term continuous phenotyping of mouse cognition and behavior; Cell Reports Methods 2023, Julija Krupic and colleagues used BrainSaw at the AMF
• Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas; PLoS Biol 2022, from Carl Petersen’s Lab, BrainSaw and StitchIt
• 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; Frontiers in Neuroanatomy 2022, from Carl Petersen’s Lab, BrainSaw and StitchIt
• Dendritic Domain-Specific Sampling of Long-Range Axons Shapes Feedforward and Feedback Connectivity of L5 Neurons; Journal of Neuroscience 2022, from Ede Rancz’s Lab, BrainSaw and StitichIt
• Tissue compartmentalization enables Salmonella persistence during chemotherapy; PNAS 2021, StitchIt
• Anatomically and functionally distinct thalamocortical inputs to primary and secondary mouse whisker somatosensory cortices; Nature Communications 2020, From Carl Petersen’s Lab. 2020, BrainSaw clone. StitchIt
• Distinct Contributions of Whisker Sensory Cortex and Tongue-Jaw Motor Cortex in a Goal-Directed Sensorimotor Transformation; Neuron 2019 From Carl Petersen’s Lab, BrainSaw clone. StitchIt