3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons
Autor: | Rainer W. Friedrich, Adrian A. Wanner, Christel Genoud |
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Jazyk: | angličtina |
Rok vydání: | 2016 |
Předmět: |
0301 basic medicine
Statistics and Probability Data Descriptor Computer science Library and Information Sciences Tracing computer.software_genre Neural circuits Education 03 medical and health sciences Olfactory bulb Imaging Three-Dimensional Voxel Microscopy medicine Biological neural network Animals Computer vision Zebrafish computer.programming_language Neurons business.industry Python (programming language) Computer Science Applications Visualization 030104 developmental biology medicine.anatomical_structure Microscopy Electron Scanning Neuron Artificial intelligence Statistics Probability and Uncertainty business computer Scanning electron microscopy Information Systems |
Zdroj: | Scientific Data |
ISSN: | 2052-4463 |
Popis: | Large-scale reconstructions of neuronal populations are critical for structural analyses of neuronal cell types and circuits. Dense reconstructions of neurons from image data require ultrastructural resolution throughout large volumes, which can be achieved by automated volumetric electron microscopy (EM) techniques. We used serial block face scanning EM (SBEM) and conductive sample embedding to acquire an image stack from an olfactory bulb (OB) of a zebrafish larva at a voxel resolution of 9.25×9.25×25 nm3. Skeletons of 1,022 neurons, 98% of all neurons in the OB, were reconstructed by manual tracing and efficient error correction procedures. An ergonomic software package, PyKNOSSOS, was created in Python for data browsing, neuron tracing, synapse annotation, and visualization. The reconstructions allow for detailed analyses of morphology, projections and subcellular features of different neuron types. The high density of reconstructions enables geometrical and topological analyses of the OB circuitry. Image data can be accessed and viewed through the neurodata web services ( http://www.neurodata.io ). Raw data and reconstructions can be visualized in PyKNOSSOS. Machine-accessible metadata file describing the reported data (ISA-Tab format) |
Databáze: | OpenAIRE |
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