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A list of techniques, protocols, assays, methods, generated from the Assay and Protocol categories

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Definition Synonym SuperCategory Has role RelatedTo
3D T1 Weighted Scan T1 weighted protocol
4Pi microscopy Imaging assay that utilizes a 4Pi microscope, a laser scanning fluorescence microscope with an improved axial resolution. The typical value of 500–700 nm can be improved to 100–150 nm, which corresponds to an almost spherical focal spot with 5–7 times less volume than that of standard confocal microscopy. The improvement in resolution is achieved by using two opposing objective lenses both of which focused to the same geometrical location. Also the difference in optical path length through each of the two objective lenses is carefully aligned to be minimal. By this, molecules residing in the common focal area of both objectives can be illuminated coherently from both sides and also the reflected or emitted light can be collected coherently, i.e. coherent superposition of emitted light on the detector is possible. (adapted from Wikipedia: http://en.wikipedia.org/wiki/Super-resolution_microscopy#4Pi) Optical imaging protocol Super-resolution microscopy
Amperometric electrode recording protocol Micro-electrode recording protocol Electrophysiology concept
Application programming interface Data access protocol
Array tomography Imaging protocol that employs methods for constructing and repeatedly staining and imaging ordered arrays of ultrathin (50–200 nm), resin-embedded serial sections on glass microscope slides,followed by electron microscopic imaging and 3D reconstruction. Microscopic imaging assay
Array tomography Imaging protocol that employs methods for constructing and repeatedly staining and imaging ordered arrays of ultrathin (50–200 nm), resin-embedded serial sections on glass microscope slides,followed by electron microscopic imaging and 3D reconstruction. Microscopic imaging assay
Arterial spin labeling magnetic resonance imaging protocol Flow-weighted magnetic resonance imaging protocol
Atomic force microscopy Utilizing a scanning probe to image and analyze the surface of a material with atomic-level resolution. Microscopic imaging assay
Autoradiography protocol A technique that uses X- ray film to locate radioactively labeled molecules or fragments of molecules by recording on a photographic plate or emulsion the radiation emitted by radioactive material within the object. (adapted from NCI) Radiolabeling protocol
Biochemical specimen preparation protocol Specimen preparation protocol
Biofeedback The process of becoming aware of various physiological functions using instruments that provide information on the activity of those same systems, with a goal of being able to manipulate them at will Protocol Electrophysiology concept
Bright-field imaging protocol Light transmission optical imaging protocol
Bright-field transmission optical imaging protocol
Cell viability assay A cellular assay used to determine cell viability in an experimental setting; the capability of developing, growing, and otherwise sustaining life (Eagle i Resource Ontology). Assay Cell viability
Cell-attached single-channel recording protocol Ion channel recording protocol Electrophysiology concept
Cell-detached inside-out single-channel recording protocol Cell-detached single-channel recording protocol Electrophysiology concept
Cell-detached outside-out single-channel recording protocol Cell-detached single-channel recording protocol Electrophysiology concept
Cell-detached single-channel recording protocol excised patch Ion channel recording protocol Electrophysiology concept
Chromatin immunoprecipitation assay is an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. Chromatin immunoprecipitation Immunoprecipitation assay
Clarity A method for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Clarity protocol Specimen preparation protocol Resource:Clarity resources
Client program software client Data access protocol
Computer Axial Tomography imaging assay CT scan
CAT scan
CT imaging
Imaging assay Neuroimaging
Computer Axial Tomography imaging protocol CAT imaging protocol
CT Imaging protocol
X-ray imaging protocol
Confocal imaging protocol confocal imaging
confocal microscopy
Light emitting optical imaging protocol
Contrast enhancement protocol Protocol designed to add contrast to a biological organism or specimen for the purposes of imaging Specimen preparation protocol Microscopy
Cuff-electrode recording protocol Suction electrode recording protocol Macro-electrode recording protocol Electrophysiology concept
Current clamp voltage recording protocol Intracellular electrode recording protocol Electrophysiology concept
Cut open oocyte voltage clamp recording protocol A technique to measure the ion currents across the membrane of oocytes, while holding the membrane voltage at a set level, while using two electrodes, one holds the membrane potential steady while the other measures current and the feedback circuit used to bridge the electrodes. Multiple-electrode voltage clamp recording protocol Electrophysiology concept
Dark-field imaging protocol Light transmission optical imaging protocol
Dark-field transmission optical imaging protocol
Data access protocol Functional specification Software resource
Decerebrate preparation Experimental animal in which the brain stem is cut at the level of the midbrain. Used to study spinal reflexes. Specimen preparation protocol Electrophysiology concept
Design-based stereology A stereology method whose probes and sampling schemes are 'designed', that is, defined a priori, so that the methods are independent of the size, shape, spatial orientation, and spatial distribution of the geometrical features to be investigated (http://www.stereology.info/design-based-stereology/). Stereology
Differential interference contrast imaging protocol Differential interference contrast microscopy
Nomarski optical imaging protocol
Light transmission optical imaging protocol
Differential interference contrast optical imaging protocol Differential interference contrast microscopy
Nomarski optical imaging protocol
Diffusion kurtosis imaging protocol Diffusion-weighted magnetic resonance imaging protocol
Diffusion spectrum imaging protocol Diffusion-weighted magnetic resonance imaging protocol
Diffusion tensor imaging A magnetic resonance imaging technique that enables the measurement of the restricted diffusion of water in tissue in order to produce neural tract images instead of using this data solely for the purpose of assigning contrast or colors to pixels in a cross sectional image. It also provides useful structural information about muscle–including heart muscle–as well as other tissues such as the prostate (from Wikipedia) Diffusion tensor imaging assay Diffusion-weighted magnetic resonance imaging Neuroimaging
Diffusion-tensor imaging protocol Diffusion tensor imaging
DTI
Diffusion tensor imaging protocol
Diffusion-weighted imaging protocol
Diffusion-weighted magnetic resonance imaging A magnetic resonance imaging (MRI) method that produces in vivo images of biological tissues weighted with the local microstructural characteristics of water diffusion. The field of diffusion MRI can be understood in terms of two distinct classes of application – Diffusion Weighted MRI and Diffusion Tensor MRI. http://en.wikipedia.org/wiki/Diffusion_MRI Diffusion MRI
Diffusion-MRI
diffusion-weighted magnetic resonance imaging assay
Magnetic resonance imaging assay
Diffusion-weighted magnetic resonance imaging protocol A magnetic resonance imaging protocol that is sensitive to the diffusion of water molecules. Magnetic resonance imaging protocol Structural magnetic resonance imaging protocol role
Discontinuous single cell voltage clamp An experimental protocol that prevents the opening and closing of voltage-gated channels and removes their influence on the membrane potential. A direct measure of membrane current can be obtained with this technique by recording the current that must be generated by the voltage clamp to keep the membrane potential from changing. Electrical recording protocol Electrophysiology concept
Electrical recording assay Electrical recording Assay Electrophysiology concept Electrical recording protocol
Electrical recording protocol Electrophysiology Protocol Electrophysiology concept
Electrocardiography recording protocol Field electrode recording protocol Electrophysiology concept
Electroencephalography recording protocol Electroencephalography Field electrode recording protocol Neuroimaging
Electrophysiology concept
Electromyography surface recording protocol A macro-electrode recording technique for recording the activation signal of muscles through the use of surface electrode. EMG may also be performed intramuscularly by inserting a needle into the muscle (intramuscular EMG) Electromyography Macro-electrode recording protocol Electrophysiology concept
Electron Energy Loss Spectroscopy imaging protocol Electron Energy Loss Spectroscopy EM imaging protocol
Electron microscopic imaging assay Electron microscopy
Electron-microscopy
Microscopic imaging assay
Electron microscopy imaging protocol Imaging protocol that employs any form of electron microscopy as the imaging assay, i.e., a protocol that forms images through the use of electrons (MM). Electron microscopy imaging protocol Image acquisition protocol
Electron microscopy immunolabeling protocol Immunolabeling protocol used to localize proteins and other molecules in the electron microscope, e.g., immunogold Ultrastructural immunolabeling protocol Immunolabeling protocol Electron microscopic imaging assay
Electron tomography imaging protocol Electron microscopy imaging protocol in which the specimen is imaged as it is tilted along one or more axes. TEM imaging protocol
Electrosurgery Electrosurgery uses alternating current to achieve cutting and coagulation. The patient becomes part of the electrical circuit and current enters their body. Cautery uses direct current to coagulate. A heated wire or electrode comes in contact with tissue. Vary the voltage of the current and the pattern of electric pulses to achieve your desired cauterizing effect. Protocol Electrophysiology concept
Event related potential recording assay Electrical recording assay Electrophysiology concept
Extracellular electrode recording protocol Micro-electrode recording protocol Electrophysiology concept
Extracellular field potential A potential difference in voltage between two spatial regions, both outside of cellular membrane. Extracellular Field Electrical recording protocol Electrophysiology concept Extracellular Amplifier
Field electrode recording protocol Surface electrode recording protocol Macro-electrode recording protocol Electrophysiology concept
Filter test assay of aggregation Assay
Fixation protocol Protocol specifying steps in the preparation of in vitro or in vivo specimens for the purpose of maintaining the existing form and structure of all of the constituent elements during subsequent procedures. Specimen preparation protocol
Flow-weighted magnetic resonance imaging protocol Magnetic resonance imaging protocol Structural magnetic resonance imaging protocol role
Fluorescence labeling protocol Microscopy contrast enhancement protocol
Fluorescence molecular tomography imaging assay Imaging assay involving collection of photons from fluorescent molecules in deep tissue that propagate through tissue at multiple projections and combining these measurements tomographically to obtain the distribution of fluorochromes. Fluorescence molecular tomography
Fluorescence molecular tomography imaging
Imaging assay
Fluorescence resonance energy transfer imaging protocol FRET protocol Light emitting optical imaging protocol
Functional MRI assay fMRI
functional magnetic resonance imaging assay
functional magnetic resonance imaging
functional neuroimaging
Magnetic resonance imaging assay
Gallyas silver stain Silver staining method for revealing neurofibrillary changes in the brains of patients with Alzheimer's disease and related models, developed by F. Gallyas. Silver stain Neurofibrillary tangle
Genome-wide association study A type of study that examines genetic variation across a given genome, designed to identify genetic associations with observable traits. In human studies, this might include traits such as blood pressure or weight, or why some people get a disease or condition. (Adapted from Wikipedia) genetic association study Protocol Genome
Genomics
Golgi staining protocol Any of several methods for staining nerve cells, nerve fibers, and neuroglia in which fixed tissue is impregnated with silver nitrate and potassium dichromate resulting in the complete staining of some nerve cells while other cells are not stained at all (http://medical-dictionary.thefreedictionary.com/Golgi%27s+stain). Golgi stain
Golgi impregnation
Staining protocol
Grid electrode recording protocol Electrical recording protocol Electrophysiology concept
Ground state depletion microscopy A type of microscopy that uses the triplet state of a fluorophore as the off-state and the singlet state as the on-state, whereby an excitation laser is used to drive the fluorophores at the periphery of the singlet state molecule to the triplet state. (adapted from Wikipedia: http://en.wikipedia.org/wiki/Super-resolution_microscopy#Ground_state_depletion_.28GSD.29) Optical imaging protocol Super-resolution microscopy
High Angular Resolution Diffusion Imaging Protocol Diffusion-weighted magnetic resonance imaging protocol
High angular resolution diffusion imaging Diffusion-weighted magnetic resonance imaging
High-pressure liquid chromotography protocol HPLC protocol Protocol
Histochemical protocol Histochemistry Microscopy_contrast_enhancement_protocol
Image acquisition protocol Protocol that specifies the acquisition of imaging data Imaging
Imaging protocol
Protocol
Imaging assay Imaging Assay
Immunoadsorption Assay
Immunocytochemistry protocol immunocytochemistry Immunolabeling protocol
Immunogold protocol Immunolabeling protocol Colloidal gold
Immunohistochemical protocol A protocol that specifies the process of immunohistochemistry. Immunohistochemistry is the process of localizing proteins in cells of a tissue section exploiting the principle of antibodies binding specifically to antigens in biological tissues. It takes its name from the roots "immuno," in reference to antibodies used in the procedure, and "histo," meaning tissue (compare to immunocytochemistry). (from wikipedia) Immunolabeling protocol
Immunolabeling protocol A means of localizing particular antigens within cells or tissue where the localization depends on the interaction of the binding region of an antibody with a specific epitope. The antibody itself may carry a detectable tag, e.g., a fluorophore, or the tag may be applied through additional steps. Contrast enhancement protocol
Immunoprecipitation assay An assay by which an antigen is precipitated from solution using an antibody. Immunoprecipitation Assay
Immunoprecipitation protocol A protocol employing immunoprecipitation to separate an antigen from a solution based on antibody binding Protocol
In vivo Immunolabeling protocol An immunolabeling protocol in which the primary antibody is applied to living cells or tissues. Immunolabeling protocol
In vivo calcium imaging assay in vivo calcium imaging
in vivo Ca2+ imaging
in vivo Ca2 imaging
Assay
In-situ hybridization protocol Specimen preparation protocol
Internalization assay Assay used to study the translocation of a receptor or molecule from the membrane or extracellular space to an endocytic vesicle Assay Receptor trafficking
Intracellular electrode recording assay Intracellular electrode recording
intracellular recording
Micro-electrode recording assay Electrophysiology concept
Intracellular electrode recording protocol Micro-electrode recording protocol Electrophysiology concept
Intracellular injection protocol Microscopy contrast enhancement protocol
Intrinsic emission imaging protocol Intrinsic emission microscopy Multiphoton imaging protocol
Ion channel recording protocol Micro-electrode recording protocol Electrophysiology concept
Ion-sensitive electrode recording protocol Amperometric electrode recording protocol Electrophysiology concept
Laser scanning confocal imaging protocol Confocal imaging protocol
Lesion A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part (adapted from NCI Metathesaurus) Specimen preparation protocol Electrophysiology concept
Light emitting optical imaging protocol fluorescence/chemiluminescence/phosphorescence optical imaging protocol Optical imaging protocol
Light microscopic imaging assay optical microscopic imaging assay
light microscopy
optical microscopy
Microscopic imaging assay
Light sheet based fluorescent microscopy imaging assay Fluorescent microscopy imaging that employs illumination in the form of a thin sheet of light directed perpendicular to the optic axis Light sheet based fluorescent microscopy
light sheet based fluorescent microscopy imaging
Light microscopic imaging assay
Light transmission optical imaging protocol Optical imaging protocol
MTT assay A colorimetric assay for measuring the activity of cellular enzymes that reduce the tetrazolium dye, MTT, to its insoluble formazan, giving a purple color. These assays measure cellular metabolic activity via NAD(P)H-dependent cellular oxidoreductase enzymes and may, under defined conditions, reflect the number of viable cells (cell proliferation). Tetrazolium dye assays can also be used to measure cytotoxicity (loss of viable cells) or cytostatic activity (shift from proliferative to resting status) of potential medicinal agents and toxic materials. (Adapted from Wikipedia: http://en.wikipedia.org/wiki/MTT_assay) Assay Cell proliferation
Cytotoxicity
Macro-electrode recording protocol Electrical recording protocol Electrophysiology concept
Macropatch voltage clamp recording protocol Single-electrode voltage clamp recording protocol Electrophysiology concept
Magnetic resonance angiography MRI-based technique used to image blood vessels. Magnetic resonance angiography is used to generate images of the arteries in order to evaluate them for stenosis (abnormal narrowing), occlusion or aneurysms (vessel wall dilatations, at risk of rupture). MRA is often used to evaluate the arteries of the neck and brain, the thoracic and abdominal aorta, the renal arteries, and the legs (called a "run-off") (from Wikipedia: http://en.wikipedia.org)/wiki/Magnetic_resonance_angiography) Magnetic resonance imaging assay
Magnetic resonance imaging A non-invasive imaging technique used in radiology to visualize internal structures of the body in detail. MRI makes use of the property of nuclear magnetic resonance (NMR) to image nuclei of atoms inside the body (adapted from Wikipedia). MRI assay
magnetic resonance imaging
MRI imaging
magnetic resonance imaging assay
nuclear magnetic resonance imaging
magnetic resonance tomography
Imaging assay Neuroimaging
Medical imaging
Magnetic resonance imaging protocol A protocol that employs magnetic resonance imaging MR imaging protocol
MRI protocol
Image acquisition protocol
Magnetic resonance spectroscopy An MR-based technique for determining the spatial concentration of metabolites in tissue. While MRI uses the signal from hydrogen protons to form anatomic images, proton MRS uses this information to determine the concentration of brain metabolites such as N-acetyl aspartate (NAA), choline (Cho), creatine (Cr) and lactate in the tissue examined. Magnetic resonance imaging assay Neuroimaging
Magnetoencephalography An imaging technique used to measure the magnetic fields produced by electrical activity in the brain via extremely sensitive devices such as superconducting quantum interference devices (SQUIDs). These measurements are commonly used in both research and clinical settings. There are many uses for the MEG, including assisting surgeons in localizing a pathology, assisting researchers in determining the function of various parts of the brain, neurofeedback, and others. - definition adapted from Wikipedia MEG Imaging assay Neuroimaging
Mass spectrometry assay A measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically. Mass spectrometry
mass spectroscopy
Assay
Micro-electrode recording assay Microelectrode recording
micro-electrode recording
Electrical recording assay Electrophysiology concept
Micro-electrode recording protocol Electrical recording protocol Electrophysiology concept
Microelectrode array assay An assay that uses a microelectrode device. A microelecrtode device contain multiple plates or shanks through which neural signals are obtained or delivered, essentially serving as neural interfaces that connect neurons to electronic circuitry. There are two general classes of MEAs: implantable MEAs, used in vivo, and non-implantable MEAs, used in vitro (adapted from Wikipedia http://en.wikipedia.org/wiki/Multielectrode_array). Micro-electrode recording assay Electrophysiology concept
Microscopic imaging assay microscopy Imaging assay
Model-based stereology A stereology method that uses models based on the geometric properties of the objects being studied (adapted from http://www.stereology.info/design-based-stereology/). Stereology
Multiphoton imaging protocol An imaging protocol that produces images using a microscopy in multiphoton mode Multiphoton microscopy
Multiphoton imaging
Two-photon imaging protocol
two-photon imaging protocol
2 photon imaging protocol
Light emitting optical imaging protocol In vivo imaging asssay Multiphoton microscope
Multiple electrode extracellular recording protocol Extracellular electrode recording protocol Electrophysiology concept
Multiple-electrode voltage clamp recording protocol Voltage clamp current recording protocol Electrophysiology concept
Myelin staining protocol Staining protocol
Neuronal tract tracing An assay in which a tracer is injected into one or more regions of the nervous system or its targets that is taken up by cells, axons or axon terminals in order to determine axonal projections to or from that region. The tract tracing assay is used to ascertain the cells of origin that innervate a brain region, the synaptic target of these cells and the route via which the axons travel in the nervous system. axonal tract tracing
neuronal tract tracing
neuronal tracing
Tract tracing protocol
Nissl staining protocol Staining protocol
Nuclear medicine imaging protocol NMR Image acquisition protocol
Optical imaging protocol An imaging protocol that uses any form of optical microscopy assay to form an image, i.e., an assay that employs light waves as the source of electromagnetic radiation. Light microscopy imaging protocol
Light microscopy
Light-microscopy
optical microscopy
Image acquisition protocol
PET imaging protocol * A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. (NCI04) (NCI) * An imaging technique using compounds labelled with short-lived positron-emitting radionuclides (such as carbon-11, nitrogen-13, oxygen-15 and fluorine-18) to measure cell metabolism. It has been useful in study of soft tissues such as CANCER; CARDIOVASCULAR SYSTEM; and BRAIN. SPECT is closely related to PET, but uses isotopes with longer half-lives and resolution is lower. (MSH) * For this type of scan, a person is given a substance that reacts with tissues in the body to release protons (parts of an atom). Through measuring the different amounts of protons released by healthy and cancerous tissues, a computer creates a picture of the inside of the body. PET images show the chemical functioning of an organ or tissue, unlike X-ray, CT, or MRI which show only body structure. Also called PET scan. (NCI) * detection of gamma rays emitted from tissues after administration of a natural substance such as glucose or fatty acids into which positron emitting isotopes have been incorporated; the paths of the gamma rays, which result from collisions of positrons and electrons, are interpreted by a computer algorithm, and the resultant tomogram represents local concentrations of the isotope containing substance. (CSP) Positron Emission Tomography imaging protocol
Positron Emission Tomography
Nuclear medicine imaging protocol
PH-sensitive electrode recording protocol Ion-sensitive electrode recording protocol Electrophysiology concept
Patch clamp technique A method for recording the electrical activity of neurons or small pathes of membrane by forming a tight seal between electrode and membrane Patching
patch
Electrical recording protocol Electrophysiology concept
Phase contrast imaging protocol Phase contrast microscopy Light transmission optical imaging protocol
Photoactivated localization microscopy A light microscopic imaging assay that builds up an image from many dark fluorophores that can be photoactivated into a fluorescing state by a flash of light. Because photoactivation is stochastic, only a few, well separated molecules "turn on." Then Gaussians are fit to their PSFs to high precision. After the few bright dots photobleach, another flash of the photoactivating light activates random fluorophores again and the PSFs are fit of these different well spaced objects. This process is repeated many times, building up an image molecule-by-molecule; and because the molecules were localized at different times, the "resolution" of the final image can be much higher than that limited by diffraction. (Adapted from Wikipedia) Photoactivated localization microscopy imaging
PALM imaging
photo-activated localization microscopy
Optical imaging protocol Super-resolution microscopy
Polarization contrast imaging protocol Polarization microscopy Light transmission optical imaging protocol
Q-ball imaging protocol Diffusion-weighted magnetic resonance imaging protocol
Rabies-virus-mediated tracing protocol Transynaptic, retrograde tracing protocol that uses a modified rabies virus to trace neuronal circuitry from its source rabies virus mediated tracing Neuronal tract tracing Transynaptic retrograde tracing protocol Retrograde tracing protocol
Transynaptic tracing protocol
Radiolabeling protocol Microscopy contrast enhancement protocol
Reconstituted bilayer electrical recording protocol Electrical recording protocol Electrophysiology concept
Reconstituted bilayer single-channel patch recording protocol Procedure by which a part of cellular membrane is recorded from. The notion is to isolate a single or at least a small number of channels in a "patch" of membrane. patch recording
patch clamp
Ion channel recording protocol Electrophysiology concept
SEM imaging protocol Scanning electron microscopy imaging protocol Electron microscopy imaging protocol
SPECT imaging protocol * A method of computed tomography that uses radionuclides which emit a single photon of a given energy. The camera is rotated 180 or 360 degrees around the patient to capture images at multiple positions along the arc. The computer is then used to reconstruct the transaxial, sagittal, and coronal images from the 3-dimensional distribution of radionuclides in the organ. The advantages of SPECT are that it can be used to observe biochemical and physiological processes as well as size and volume of the organ. The disadvantage is that, unlike positron-emission tomography where the positron-electron annihilation results in the emission of 2 photons at 180 degrees from each other, SPECT requires physical collimation to line up the photons, which results in the loss of many available photons and hence degrades the image. (MSH) * method of computed tomography that uses radionuclides which emit a single photon of a given energy: the camera is rotated 180 or 360 degrees around the subject to capture images at multiple positions along the arc; the computer is then used to reconstruct the transaxial, sagittal, and coronal images from the three-dimensional distribution of radionuclides in the organ. (CSP) Single Photon Emission Computed Tomography imaging protocol
Single Photon Emission Computed Tomography
Nuclear medicine imaging protocol Neuroimaging
STEM imaging protocol Scanning transmission electron microscopy imaging protocol Electron microscopy imaging protocol
Sarkosyl solubility assay Assay
Scanning electron microscopic imaging assay Electron microscopic imaging assay where the image is formed by scanning an electron beam across a sample in a scanning electron microscope, and collecting scattered electrons to form an image. The signals result from interactions of the electron beam with atoms at or near the surface of the sample. In the most common or standard detection mode, secondary electron imaging or SEI, the SEM can produce very high-resolution images of a sample surface, revealing details about less than 1 to 5 nm in size. Due to the very narrow electron beam, SEM micrographs have a large depth of field yielding a characteristic three-dimensional appearance useful for understanding the surface structure of a sample. (adapted from Wikipedia; http://en.wikipedia.org/wiki/Scanning_electron_microscopy) Scanning electron microscopy Electron microscopic imaging assay
Serial block face scanning electron microscopic imaging assay Scanning electron microscopy assay that combines automated block-face imaging with serial sectioning inside the chamber of a scanning electron microscope and uses backscattering contrast to visualize the heavy-metal staining of tissue (adapted from Denk and Horstmann, PLoS Biol. 2004 Nov;2(11):e329, 2004). serial block face imaging
serial block face SEM
serial block face scanning electron microscopy
Scanning electron microscopic imaging assay
Silver stain Staining method that uses silver to selectively alter the appearance of a target in microscopy of histological sections; in temperature gradient gel electrophoresis; and in polyacrylamide gels (adapted from Wikipedia: http://en.wikipedia.org/wiki/Silver_stain) Staining protocol
Single electrode extracellular recording protocol Extracellular electrode recording protocol Electrophysiology concept
Single tilt electron tomography imaging protocol Electron tomography protocol where the specimen is imaged at intervals as it is rotated along a single axis Electron tomography imaging protocol
Single-electrode voltage clamp recording protocol Voltage clamp current recording protocol Electrophysiology concept
Slice preparation protocol Protocol in which slices of tissue are excised from an animal and kept alive in vitro. Slice preparation Specimen preparation protocol Electrophysiology concept
Somatic reprogramming protocol Protocol Stem cell
Specimen preparation protocol Protocol
Spectroscopic magnetic resonance imaging protocol Magnetic resonance spectroscopic imaging
MRS imaging
Magnetic resonance imaging protocol
Spectroscopic optical imaging protocol Spectroscopic microscopy Light emitting optical imaging protocol
Staining protocol Microscopy contrast enhancement protocol
Static HTML document Web page
Stereology An imaging assay that is used for the three-dimensional interpretation of planar sections of materials or tissues (Eagle i Resource Ontology: http://purl.obolibrary.org/obo/ERO_0001360) unbiased stereology Imaging assay Cell counting
Stimulated emission depletion microscopy A light microscopic imaging protocol that uses simulated emission depletion microscopy, a type of microscopy that uses two laser pulses, the excitation pulse for excitation of the fluorophores to their fluorescent state and the STED pulse for the de-excitation of fluorophores by means of stimulated emission (adapted from Wikipedia (http://en.wikipedia.org/wiki/Super-resolution_microscopy#Stimulated_emission_depletion_.28STED.29) Stimulated emission depletion microscopy
Stimulated emission depletion imaging
STED imaging
Optical imaging protocol Super-resolution microscopy
Surgical protocol Protocol Electrophysiology concept
T1-weighted magnetic resonance imaging protocol T1 weighted imaging protocol
T1 imaging protocol
Magnetic resonance imaging protocol Structural magnetic resonance imaging protocol role
T2-weighted magnetic resonance imaging protocol T2 weighted protocol Magnetic resonance imaging protocol Structural magnetic resonance imaging protocol role
TEM imaging protocol Transmission electron microscopy imaging protocol Electron microscopy imaging protocol
Timm's stain A staining technique used to visualize a variety of metals in brains and other tissues, including trace metals essential for life, such as Zn, Cu, Fe, Co, and Ni, as well as toxic metals, e.g., Hg, Cd, Pb, As, Bi, TI, Au and Ag. This method, originally developed by Timm (1958), was later modified. The technique is based on sulphide-precipitation of metals in tissue followed by a physical development. During the latter stage the metal sulphides catalyze the reduction of silver ions by reducing agents. This technique has proven to be particularly useful in visualizing zinc-containing neurons and the detection of newly sprouted axons and axon terminals within the central nervous system (Adapted from (http://www.neurodigitech.com/services/210403.html) Timm's sulfide silver staining
Timm's method
Silver stain Zinc(2+)
Total internal reflection imaging protocol Total internal reflection microscopy Light transmission optical imaging protocol
Total internal reflection optical imaging protocol Total internal reflection microscopy
Tract tracing protocol Methods used to determine connectivity between brain structures or neuron populations Protocol Connectivity
Tractography a 3D modeling technique used to investigate and visualize neural tracts using data collected by diffusion tensor imaging (DTI). It uses special techniques of magnetic resonance imaging (MRI), and computer-based image analysis. The results are presented in two- and three-dimensional images (modified from Wikipedia). tractography protocol Tract tracing protocol Diffusion tensor imaging
Connectivity
Transmission electron microscopic imaging assay transmission electron microscopy Electron microscopic imaging assay
Trypan Blue exclusion assay Cell viability assay involving application of trypan blue. Live cells or tissues with intact cell membranes are not stained while dead cells absorb the stain and are shown as a distinctive blue colour under a microscope. Since live cells are excluded from staining, this staining method is also described as a dye exclusion method (adapted from Wikipedia http://en.wikipedia.org/wiki/Trypan_blue). Cell viability assay Trypan Blue
Two electrode voltage clamp recording protocol A technique to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level, while using two electrodes, one holds the membrane potential steady while the other measures current and the feedback circuit used to bridge the electrodes. Two electrode voltage clamp Multiple-electrode voltage clamp recording protocol Electrophysiology concept
Ultrasonographic imaging protocol * RAEB: The visualization of deep structures of the body by recording the reflections of echoes of pulses of ultrasonic waves directed into the tissues. Use of ultrasound for imaging or diagnostic purposes employs frequencies ranging from 1.6 to 10 megahertz. (MSH99) (NCI) * The visualization of deep structures of the body by recording the reflections of echoes of pulses of ultrasonic waves directed into the tissues. Use of ultrasound for imaging or diagnostic purposes employs frequencies ranging from 1.6 to 10 megahertz. (MSH) * Use of ultrasound for imaging or diagnostic purposes. Employs frequencies ranging from 1.6 to 10 megahertz. (DCTD-DIP) (NCI) * high frequency sound waves used to identify and examine internal organs and structures without the invasive hazards of X xays, dyes, or fluoroscopy. (CSP) Echography
Ultrasonography
Ultrasonic imaging protocol
Sonography
Ultrasound imaging protocol
Ultrasound imaging procedure
Image acquisition protocol
Voltage clamp current recording protocol Intracellular electrode recording protocol Electrophysiology concept
Voxelation Method for high-throughput acquisition of three-dimensional gene expression patterns in the brain through analysis of spatially registered voxels (cubes). The method results in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging techniques. Assay Gene expression
Web service A resource that provides a software system designed to support interoperable machine-to-machine interaction over a network. Web services are frequently Web APIs that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services.


NITRC definition: Specific functions provided to applications via standard Internet protocols (XML, SOAP, WSDL, UDDI).
Data access protocol
Western blot assay Assay for identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes (adapted from MESH). Western blot
immunoblot
Assay Western blot protocol
Western blot protocol A protocol that uses a Western blot assay to identify and quantify a binder protein interaction. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane. (Adapted from the Protein Affinity Reagent ontology) Protocol
Whole-cell voltage clamp recording protocol Single-electrode voltage clamp recording protocol Electrophysiology concept
Wide-field fluorescence imaging protocol Light emitting optical imaging protocol
X ray microscopy protocol An X ray imaging protocol that employs X ray microscopy to form an image, i.e., a type of microscopy that employs soft X rays as the electromagnetic radiation source that forms the image (adapted from Wikipedia: http://en.wikipedia.org/wiki/X-ray_microscope). X-ray imaging protocol
X-ray crystallography A molecular assay used to determine the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and diffracts into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder and various other information (Eagle-i Resource Ontology) Crystallography
X ray crystallography
X ray crystallography assay
Assay Atomic structure determination
X-ray imaging protocol Imaging protocol that employs an X-ray imaging assay to form images, i.e., an an imaging assay that uses X rays as the electromagnetic radiation source (MM) Image acquisition protocol

Contributors

Akash, Memartone



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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.