Biomaterial Database

Challenges of microtome-based serial block-face scanning electron microscopy in neuroscience. 2015

A A Wanner, and M A Kirschmann, and C Genoud

Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland.

Serial block-face scanning electron microscopy (SBEM) is becoming increasingly popular for a wide range of applications in many disciplines from biology to material sciences. This review focuses on applications for circuit reconstruction in neuroscience, which is one of the major driving forces advancing SBEM. Neuronal circuit reconstruction poses exceptional challenges to volume EM in terms of resolution, field of view, acquisition time and sample preparation. Mapping the connections between neurons in the brain is crucial for understanding information flow and information processing in the brain. However, information on the connectivity between hundreds or even thousands of neurons densely packed in neuronal microcircuits is still largely missing. Volume EM techniques such as serial section TEM, automated tape-collecting ultramicrotome, focused ion-beam scanning electron microscopy and SBEM (microtome serial block-face scanning electron microscopy) are the techniques that provide sufficient resolution to resolve ultrastructural details such as synapses and provides sufficient field of view for dense reconstruction of neuronal circuits. While volume EM techniques are advancing, they are generating large data sets on the terabyte scale that require new image processing workflows and analysis tools. In this review, we present the recent advances in SBEM for circuit reconstruction in neuroscience and an overview of existing image processing and analysis pipelines.

UI	MeSH Term	Description	Entries
D008855	Microscopy, Electron, Scanning	Microscopy in which the object is examined directly by an electron beam scanning the specimen point-by-point. The image is constructed by detecting the products of specimen interactions that are projected above the plane of the sample, such as backscattered electrons. Although SCANNING TRANSMISSION ELECTRON MICROSCOPY also scans the specimen point by point with the electron beam, the image is constructed by detecting the electrons, or their interaction products that are transmitted through the sample plane, so that is a form of TRANSMISSION ELECTRON MICROSCOPY.	Scanning Electron Microscopy,Electron Scanning Microscopy,Electron Microscopies, Scanning,Electron Microscopy, Scanning,Electron Scanning Microscopies,Microscopies, Electron Scanning,Microscopies, Scanning Electron,Microscopy, Electron Scanning,Microscopy, Scanning Electron,Scanning Electron Microscopies,Scanning Microscopies, Electron,Scanning Microscopy, Electron
D008867	Microtomy	The technique of using a microtome to cut thin or ultrathin sections of tissues embedded in a supporting substance. The microtome is an instrument that hold a steel, glass or diamond knife in clamps at an angle to the blocks of prepared tissues, which it cuts in sections of equal thickness.	Thin Sectioning,Ultramicrotomy,Sectioning, Thin,Sectionings, Thin,Thin Sectionings
D009434	Neural Pathways	Neural tracts connecting one part of the nervous system with another.	Neural Interconnections,Interconnection, Neural,Interconnections, Neural,Neural Interconnection,Neural Pathway,Pathway, Neural,Pathways, Neural
D009474	Neurons	The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the NERVOUS SYSTEM.	Nerve Cells,Cell, Nerve,Cells, Nerve,Nerve Cell,Neuron
D009488	Neurosciences	The scientific disciplines concerned with the embryology, anatomy, physiology, biochemistry, pharmacology, etc., of the nervous system.	Neuroscience
D001921	Brain	The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.	Encephalon
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D013569	Synapses	Specialized junctions at which a neuron communicates with a target cell. At classical synapses, a neuron's presynaptic terminal releases a chemical transmitter stored in synaptic vesicles which diffuses across a narrow synaptic cleft and activates receptors on the postsynaptic membrane of the target cell. The target may be a dendrite, cell body, or axon of another neuron, or a specialized region of a muscle or secretory cell. Neurons may also communicate via direct electrical coupling with ELECTRICAL SYNAPSES. Several other non-synaptic chemical or electric signal transmitting processes occur via extracellular mediated interactions.	Synapse
D016591	Histocytological Preparation Techniques	Methods of preparing cells or tissues for examination and study of their origin, structure, function, or pathology. The methods include preservation, fixation, sectioning, staining, replica, or other technique to allow for viewing using a microscope.	Cytohistological Preparation Techniques,Cytohistologic Preparation Technics,Cytohistologic Preparation Technique,Cytohistologic Preparation Techniques,Cytohistological Preparation Technic,Cytohistological Preparation Technics,Cytohistological Preparation Technique,Histocytologic Preparation Technic,Histocytologic Preparation Technics,Histocytologic Preparation Technique,Histocytologic Preparation Techniques,Histocytological Preparation Technic,Histocytological Preparation Technics,Histocytological Preparation Technique,Preparation Technic, Cytohistologic,Preparation Technic, Cytohistological,Preparation Technic, Histocytologic,Preparation Technic, Histocytological,Preparation Technics, Cytohistologic,Preparation Technics, Cytohistological,Preparation Technics, Histocytologic,Preparation Technics, Histocytological,Preparation Technique, Cytohistologic,Preparation Technique, Cytohistological,Preparation Technique, Histocytologic,Preparation Technique, Histocytological,Preparation Techniques, Cytohistologic,Preparation Techniques, Cytohistological,Preparation Techniques, Histocytologic,Preparation Techniques, Histocytological,Technic, Cytohistologic Preparation,Technic, Cytohistological Preparation,Technic, Histocytologic Preparation,Technic, Histocytological Preparation,Technics, Cytohistologic Preparation,Technics, Cytohistological Preparation,Technics, Histocytologic Preparation,Technics, Histocytological Preparation,Technique, Cytohistologic Preparation,Technique, Cytohistological Preparation,Technique, Histocytologic Preparation,Technique, Histocytological Preparation,Techniques, Cytohistologic Preparation,Techniques, Cytohistological Preparation,Techniques, Histocytologic Preparation,Techniques, Histocytological Preparation,Cytohistologic Preparation Technic
D021621	Imaging, Three-Dimensional	The process of generating three-dimensional images by electronic, photographic, or other methods. For example, three-dimensional images can be generated by assembling multiple tomographic images with the aid of a computer, while photographic 3-D images (HOLOGRAPHY) can be made by exposing film to the interference pattern created when two laser light sources shine on an object.	Computer-Assisted Three-Dimensional Imaging,Imaging, Three-Dimensional, Computer Assisted,3-D Image,3-D Imaging,Computer-Generated 3D Imaging,Three-Dimensional Image,Three-Dimensional Imaging, Computer Generated,3 D Image,3 D Imaging,3-D Images,3-D Imagings,3D Imaging, Computer-Generated,3D Imagings, Computer-Generated,Computer Assisted Three Dimensional Imaging,Computer Generated 3D Imaging,Computer-Assisted Three-Dimensional Imagings,Computer-Generated 3D Imagings,Image, 3-D,Image, Three-Dimensional,Images, 3-D,Images, Three-Dimensional,Imaging, 3-D,Imaging, Computer-Assisted Three-Dimensional,Imaging, Computer-Generated 3D,Imaging, Three Dimensional,Imagings, 3-D,Imagings, Computer-Assisted Three-Dimensional,Imagings, Computer-Generated 3D,Imagings, Three-Dimensional,Three Dimensional Image,Three Dimensional Imaging, Computer Generated,Three-Dimensional Images,Three-Dimensional Imaging,Three-Dimensional Imaging, Computer-Assisted,Three-Dimensional Imagings,Three-Dimensional Imagings, Computer-Assisted