Szi-chieh Yu
A5014758925- Neural dynamics and brain function
- Neurobiology and Insect Physiology Research
- Neuroscience and Neuropharmacology Research
- Photoreceptor and optogenetics research
- Genetics, Aging, and Longevity in Model Organisms
- Cell Image Analysis Techniques
- Insect and Arachnid Ecology and Behavior
- Advanced Electron Microscopy Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Advanced Memory and Neural Computing
- Physiological and biochemical adaptations
- Functional Brain Connectivity Studies
- Circadian rhythm and melatonin
- Plant and Biological Electrophysiology Studies
- Retinal Development and Disorders
- Neuroinflammation and Neurodegeneration Mechanisms
- Visual perception and processing mechanisms
- Cellular transport and secretion
- Plant and animal studies
- Zebrafish Biomedical Research Applications
- Software System Performance and Reliability
- Advanced Neuroimaging Techniques and Applications
- Evolutionary Game Theory and Cooperation
Princeton University
2019-2025
Neuroscience Institute
2021-2023
Goethe University Frankfurt
2015-2021
University of Illinois Chicago
2011
Abstract Connections between neurons can be mapped by acquiring and analyzing electron microscopic (EM) brain images. In recent years, this approach has been applied to chunks of brains reconstruct local connectivity maps that are highly informative, yet inadequate for understanding function more globally. Here, we present the first neuronal wiring diagram a whole adult brain, containing 5×10 7 chemical synapses ∼130,000 reconstructed from female Drosophila melanogaster . The resource also...
High-resolution electron microscopy of nervous systems has enabled the reconstruction synaptic connectomes. However, we do not know sign for each connection (i.e., whether a is excitatory or inhibitory), which implied by released transmitter. We demonstrate that artificial neural networks can predict transmitter types presynapses from micrographs: network trained to six transmitters (acetylcholine, glutamate, GABA, serotonin, dopamine, octopamine) achieves an accuracy 87% individual...
Abstract The fruit fly Drosophila melanogaster combines surprisingly sophisticated behaviour with a highly tractable nervous system. A large part of the fly’s success as model organism in modern neuroscience stems from concentration collaboratively generated molecular genetic and digital resources. As presented our FlyWire companion paper 1 , this now includes first full brain connectome an adult animal. Here we report systematic hierarchical annotation ∼130,000-neuron including neuronal...
Learning from experience depends at least in part on changes neuronal connections. We present the largest map of connectivity to date between cortical neurons a defined type (layer 2/3 [L2/3] pyramidal cells mouse primary visual cortex), which was enabled by automated analysis serial section electron microscopy images with improved handling image defects (250 × 140 90 μm3 volume). used identify constraints learning algorithms employed cortex. Previous studies modeled continuum synapse sizes...
Abstract Understanding the brain requires understanding neurons’ functional responses to circuit architecture shaping them. Here we introduce MICrONS connectomics dataset with dense calcium imaging of around 75,000 neurons in primary visual cortex (VISp) and higher areas (VISrl, VISal VISlm) an awake mouse that is viewing natural synthetic stimuli. These data are co-registered electron microscopy reconstruction containing more than 200,000 cells 0.5 billion synapses. Proofreading a subset...
Abstract Mammalian neocortex contains a highly diverse set of cell types. These types have been mapped systematically using variety molecular, electrophysiological and morphological approaches 1–4 . Each modality offers new perspectives on the variation biological processes underlying cell-type specialization. Cellular-scale electron microscopy provides dense ultrastructural examination an unbiased perspective subcellular organization brain cells, including their synaptic connectivity...
Abstract Understanding the relationship between circuit connectivity and function is crucial for uncovering how brain computes. In mouse primary visual cortex, excitatory neurons with similar response properties are more likely to be synaptically connected 1–8 ; however, broader rules remain unknown. Here we leverage millimetre-scale MICrONS dataset analyse synaptic functional of across cortical layers areas. Our results reveal that preferentially within areas—including feedback...
Neural circuit function is shaped both by the cell types that comprise and connections between them1. have previously been defined morphology2,3, electrophysiology4, transcriptomic expression5,6, connectivity7-9 or a combination of such modalities10-12. The Patch-seq technique enables characterization morphology, electrophysiology properties from individual cells13-15. These were integrated to define 28 inhibitory, morpho-electric-transcriptomic (MET) in mouse visual cortex16, which do not...
We are in the era of millimetre-scale electron microscopy volumes collected at nanometre resolution1,2. Dense reconstruction cellular compartments these has been enabled by recent advances machine learning3-6. Automated segmentation methods produce exceptionally accurate reconstructions cells, but post hoc proofreading is still required to generate large connectomes that free merge and split errors. The elaborate 3D meshes neurons contain detailed morphological information multiple scales,...
Abstract High-resolution electron microscopy of nervous systems enables the reconstruction connectomes. A key piece missing information from connectomes is synaptic sign. We show that for D. melanogaster , artificial neural networks can predict transmitter type released at synapses micrographs and thus add putative signs to connections. Our network discriminates between six transmitters (acetylcholine, glutamate, GABA, serotonin, dopamine, octopamine) with an average accuracy 87%/94%...
Understanding the relationship between circuit connectivity and function is crucial for uncovering how brain implements computation. In mouse primary visual cortex (V1), excitatory neurons with similar response properties are more likely to be synaptically connected, but previous studies have been limited within V1, leaving much unknown about broader rules. this study, we leverage millimeter-scale MICrONS dataset analyze synaptic functional of individual across cortical layers areas. Our...
In most complex nervous systems there is a clear anatomical separation between the nerve cord, which contains of final motor outputs necessary for behaviour, and brain. insects, neck connective both physical information bottleneck connecting brain ventral cord (VNC, spinal analogue) comprises diverse populations descending (DN), ascending (AN) sensory neurons, are crucial sensorimotor signalling control. Integrating three separate EM datasets, we now provide complete connectomic description...
Abstract Learning from experience depends at least in part on changes neuronal connections. We present the largest map of connectivity to date between cortical neurons a defined type (L2/3 pyramidal cells), which was enabled by automated analysis serial section electron microscopy images with improved handling image defects. used identify constraints learning algorithms employed cortex. Previous studies modeled continuum synapse sizes (Arellano et al. 2007) log-normal distribution...
Abstract To understand the brain we must relate neurons’ functional responses to circuit architecture that shapes them. Here, present a large connectomics dataset with dense calcium imaging of millimeter scale volume. We recorded activity from approximately 75,000 neurons in primary visual cortex (VISp) and three higher areas (VISrl, VISal VISlm) an awake mouse viewing natural movies synthetic stimuli. The data were co-registered volumetric electron microscopy (EM) reconstruction containing...
Abstract 3D electron microscopy (EM) has been successful at mapping invertebrate nervous systems, but the approach limited to small chunks of mammalian brains. To scale up larger volumes, we have built a computational pipeline for processing petascale image datasets acquired by serial section EM, popular form EM. The employs convolutional nets compute nonsmooth transformations required align images sections containing numerous cracks and folds, detect neuronal boundaries, label voxels as...
Abstract Brains comprise complex networks of neurons and connections. Network analysis applied to the wiring diagrams brains can offer insights into how support computations regulate information flow. The completion first whole-brain connectome an adult Drosophila , largest date, containing 130,000 millions connections, offers unprecedented opportunity analyze its network properties topological features. To gain local connectivity, we computed prevalence two- three-node motifs, examined...