makes_use_of
The child is an essential component of the parent device, or plays an essential role in performance of the parent function.
Is a
dummy term
sample preparation method
chemically fixed tissue
coagulating-fixative fixed tissue
acetone fixed tissue
acrolein fixed tissue
ethanol fixed tissue
methanol fixed tissue
crosslinking-fixative fixed tissue
ethylene glycol-bis-succinimidyl succinate fixed tissue
EGS
formaldehyde fixed tissue
glutaraldehyde fixed tissue
osmium tetroxide fixed tissue
cryofixed tissue
unfixed tissue
embedded tissue
tissue in plastic embedment
tissue in acrylic resin embedment
tissue in epoxy resin embedment
tissue in wax embedment
tissue in paraffin embedment
tissue in polyester wax embedment
tissue in polyethylene glycol embedment
unembedded tissue
whole mounted tissue
living tissue
live-cell imaging
Unfixed fully hydrated tissue, typically employed to monitor dynamic changes in the living state.
sectioned tissue
cryostat-sectioned tissue
hand-sectioned tissue
microtome-sectioned tissue
vibratome-sectioned tissue
visualization method
endogenous substrate, non-vital dye
diagram
HA peptide tag
cresyl fast violet
endogenous substrate, diaminobenzidine
eosin
Staining with an aqueous or alcoholic solution of eosin Y,colors eosinophilic structures in various shades of red, pink and orange. The eosinophilic structures are generally composed of intracellular or extracellular protein. The Lewy bodies and Mallory bodies are examples of eosinophilic structures. Most of the cytoplasm is eosinophilic. Red blood cells are stained intensely red.
ethidium bromide
fuchsin
giemsa
hematoxylin
The staining method involves application of hemalum, which is a complex formed from aluminium ions and oxidized haematoxylin. This colors nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The staining of nuclei by hemalum does not require the presence of DNA and is probably due to binding of the dye-metal complex to arginine-rich basic nucleoproteins such as histones. The mechanism is different from that of nuclear staining by basic (cationic) dyes such as thionine or toluidine blue. Staining by basic dyes is prevented by chemical or enzymatic extraction of nucleic acids. Such extractions do not prevent staining of nuclei by hemalum.
methyl green
methyl violet
nitro blue tetrazolium chloride
nuclear fast red
orcein
propidium iodide
SYTOX Green
toluidine blue
endogenous substrate, vital dye
acridine orange
Hoechst 33342
HO342
cationic colloidal gold
CMX rosamine (Mitotracker Red)
Mitotracker X
DiOC6 (3,3'-dihexyloxacarbocyanine iodide)
DiOC
4',6-diamidino-2-phenylindole (DAPI)
DAPI
lucifer yellow
methylene blue
Nile blue A
Nile red
pyronine
rhodamine 123
rhodamine B
SYTO Blue
SYTO Green
SYTO Orange
SYTO Red
YO-PRO-1
endogenous substrate, dye conjugate
endogenous substrate, acidotropic-fluor conjugate
LysoTracker
endogenous substrate, lectin-fluor conjugate
endogenous substrate, lectin-gold conjugate
taxol
endogenous substrate, phalloidin-fluor conjugate
exogenous label
genetically encoded enzyme
beta-galactosidase
lacZ, X-gal
beta-glucuronidase
GUS, X-gluc
genetically encoded tag
EBFP
BFP
ECFP
CFP
EGFP
GFP
Aequorea victoria red fluorescent protein tag
RFP
EYFP
YFP
DsRed
c-MYC peptide tag
FLAG peptide tag
intracellular filling
visualization of the connected regions of a cell by filling with a label
tissue in vitreous ice embedment
Fully hydrated tissue rapidly frozen to produce vitrified water, and maintained continuously below the glass transition temperature of water (approximately -137 deg C
tissue in amorphous ice embedment
fluor labeled RNA fill
5-SFX fluorescein RNA fill
X-rhodamine RNA fill
permeabilized tissue
Tissue treated to make cell membranes permeable, typically for the purpose of allowing access by exogenous stains or substrates.
fluor labeled protein fill
fluor conjugated actin fill
Alexa Fluor 488 actin fill
Alexa Fluor 568 actin fill
fluoresceine actin fill
rhodamine actin fill
phalloidin
Alexa Fluor 350 phalloidin fill
Alexa Fluor 488 phalloidin fill
eosin phalloidin fill
fluoresceine phalloidin fill
Oregon Green 488 phalloidin fill
Oregon Green 514 phalloidin fill
rhodamine phalloidin fill
Texas Red-X phalloidin fill
fluor conjugated tubulin fill
Oregon Green 514 tubulin fill
X-rhodamine tubulin fill
probe for lipid
DiA
DiD
DiI
DiO
DiR
miscellaneous fill
biotin ethylenediamine fill
Neurobiotin
cobalt fill
silver-intensified cobalt fill
metabolically incorporated radioisotope
label conjugated to probe
glycerol permeabilized
tissue made permeable by the action of glycerol
glycerinated tissue
labeled primary antibody
primary antibody-enzyme conjugate, substrate
alkaline phosphatase
primary antibody-alkaline phosphastase conjugate, DAB
primary antibody-alkaline phosphastase conjugate, ELF 97 phosphate
primary antibody-alkaline phosphastase conjugate, Vector Black
primary antibody-alkaline phosphastase conjugate, Vector Blue
primary antibody-alkaline phosphastase conjugate, Vector Red
horseradish peroxidase
primary antibody-horseradish peroxidase, 4-chloro-1-naphthol
primary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole
primary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine
primary antibody-horseradish peroxidase, Vector NovaRed
primary antibody-horseradish peroxidase, Vector SG
primary antibody-horseradish peroxidase, Vector VIP
primary antibody-fluor conjugate
primary antibody-aminomethylcoumarin acetate
AMCA
primary antibody-Cascade blue
primary antibody-cyanine
Cy2
primary antibody-fluorescein isothiocyanate
FITC
primary antibody-indocarbocyanine
Cy3
primary antibody-indodicarbocyanine
Cy5
primary antibody-rhodamine red-X
RRX
primary antibody-tetramethyl rhodamine isothiocyanate
TRITC
primary antibody-Texas Red
primary antibody-gold conjugate
primary antibody plus labeled secondary antibody
secondary antibody-enzyme conjugate, substrate
acid phosphatase
secondary antibody-alkaline phosphastase conjugate, DAB
secondary antibody-alkaline phosphastase conjugate, ELF 97 phosphate
secondary antibody-alkaline phosphastase conjugate, Fast Blue B
secondary antibody-alkaline phosphastase conjugate, Fast Red
secondary antibody-alkaline phosphastase conjugate, INT
secondary antibody-alkaline phosphastase conjugate, Magenta Phos
secondary antibody-alkaline phosphastase conjugate, NABP
secondary antibody-alkaline phosphastase conjugate, NAGP
secondary antibody-alkaline phosphastase conjugate, NAMP
secondary antibody-alkaline phosphastase conjugate, NATP
secondary antibody-alkaline phosphastase conjugate, NBT
secondary antibody-alkaline phosphastase conjugate, Vector Black
secondary antibody-alkaline phosphastase conjugate, Vector Blue
secondary antibody-alkaline phosphastase conjugate, Vector Red
secondary antibody-alkaline phosphastase conjugate, BCIP
secondary antibody-beta-galactosidase, X-Gal
secondary antibody-beta-glucuronidase, X-gluc
esterase
secondary antibody-esterase, Naphthol-AS-D-chloroacetate
glucose oxidase
secondary antibody-glucose oxidase, TNBT
secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine
secondary antibody-horseradish peroxidase, 3,3'-diaminobenzidine silver enhanced
secondary antibody-horseradish peroxidase, 4-chloro-1-naphthol
secondary antibody-horseradish peroxidase, 3-amino-9-ethylcarbazole
secondary antibody-horseradish peroxidase, 3,3',5,5'-tetramethylbenzidine
secondary antibody-horseradish peroxidase, Vector NovaRed
secondary antibody-horseradish peroxidase, Vector SG
secondary antibody-horseradish peroxidase, Vector VIP
secondary antibody-phosphatase, Naphthol-AS-BI-phosphate
secondary antibody-fluor conjugate
secondary antibody-Alexa Fluor conjugate
aminomethylcoumarin
Cascade blue
secondary antibody-cyanine conjugate
secondary antibody-diaminotriazinylaminoflorescein conjugate
DTAF
secondary antibody-fluorescein isothiocyanate conjugate
secondary antibody-indocarbocyanine conjugate
secondary antibody-indodicarbocyanine conjugate
secondary antibody-lissamine rhodamine sulfonyl chloride
LSRC
secondary antibody-rhodamine red-X conjugate
secondary antibody-tetramethyl rhodamine isothiocyanate conjugate
secondary antibody-Texas red conjugate
gold
labeled nucleic acid probe
DNA probe
biotin labeled DNA probe
digoxigenin labeled DNA probe
fluor labeled DNA probe
BODIPY TR-14-dUTP labeled DNA probe
bromodeoxyuridine labeled DNA probe
fluoresceine-12-dUTP labeled DNA probe
Oregon Green 488-5-dUTP labeled DNA probe
radioisotope labeled DNA probe
[32]P labeled DNA probe
[33]P labeled DNA probe
RNA probe
biotin labeled RNA probe
digoxigenin labeled RNA probe
fluoroscein labeled RNA probe
radioisotope labeled RNA probe
[32]P labeled RNA probe
[33]P labeled RNA probe
imaging method
graphic illustration
computer graphic
black and white graphic
color graphic
grey scale graphic
camera lucida assisted graphic
free hand graphic
line art graphic
charcoal pencil graphic
colored pencil graphic
graphite pencil graphic
pen and ink graphic
painted graphic
acrylic painted graphic
oil painted graphic
pastel painted graphic
watercolor painted graphic
macroscopy
methods for imaging objects large enough to be observed by the unaided eye
microscopy
methods for forming images of objects too small to be observed with the unaided eye
wide field light micrograph
bright-field microscopy
dark-field microscopy
imaging with rejection of the unscattered illumination (removal of the zero order component of the diffracted wave)
differential interference contrast microscopy
Nomarski
DIC
fluorescence microscopy
phase contrast microscopy
polarization microscopy
time lapse microscopy
narrow field light micrograph
confocal microscopy
single-spot confocal microscopy
spinning disk confocal microscopy
two-photon laser scanning microscopy
multi-photon microscopy
mode of electron microscopy
scanning electron microscopy (SEM)
image is formed by scanning the surface of the specimen with a beam of electrons in a raster pattern
transmission electron microscopy (TEM)
atomic force microscopy
the scanning probe is maintained at a fixed distance above the surface e of the specimen by van der Waals forces
X-ray micrograph
montage
detergent permeabilized
Membrane permeabilization by the action of ionic or non-ionic detergents
solvent permeabilized
permeabilization due to extraction of lipid from membranes by an organic solvent such as acetone or methanol.
saponin permeabilized
Saponin, a detergent-like molecule, preferentially forms holes in membranes that contain cholesterol.
saponized tissue
recorded image
photograph
micrograph
methods and devices used for capturing an image of a real object; distinct from images created by artwork
portrayed image
drawing
artwork
methods and devices used for creating images by some form of artwork, as distinct from capturing images by means of some recording device
animation
A form of graphical illustration that changes with time to give a sense of motion or represent dynamic changes in the portrayal.
illumination method
sources and methods for illumination
detection method
media and devices employed for recording the alterations in the illumination that result from its interaction with the sample
imaged parameter
The physical property of the specimen that leads to the modifications of the illumination that are recorded in the image.
contrast-enhancing method
illumination by photons
illumination by electrons
illumination by acoustic waves
illumination by neutrons
illumination by ions
widefield illumination
illumination that covers the entire field of view of the image-forming lens
narrowfield illumination
illumination restricted to a small portion of the field of view of the imaging lens; often one or more diffraction limited spots
coherent illumination
incoherent illumination
nearfield illumination
farfield illumination
continuous illumination
pulsed illumination
illumination that varies with time; often achieved with pulsed lasers for the purpose of generating very-high peak illumination power
oblique illumination
single point scanning
illumination by a single spot of light that is scanned across the field of view
multiple point scanning
illumination by multiple points of light simultaneously
spinning disk scanning
scanning by multiple points of light arising from pinholes in a spinning disk that is illuminated by a widefield source
array scanning
Multiple points of illumination generated by a fixed array of sources.
hollow-cone illumination
illumination parallel or at small angles to the optical axis is attenuated or blocked by a stop
anaxial illumination
Illumination is distributed asymmetrically around the optic axis, typically achieved by a non-circular stop placed below the lower lens element and aperture of the condenser.
darkfield illumination
illumination restricted to angles that exceed the acceptance angle of the image-forming lens
Rheinberg illumination
illumination at angles less than the acceptance angle of the image-forming lens is attenuated by a filter to give a colored background of unscattered light; higher angle illumination may be filtered to give a contrasting color
charge coupled device (CCD)
photomultiplier tube (PMT)
photodiode
avalanche photodiode (APD)
silicon intensified target tube (SIT)
intensified SIT (ISIT)
intensified CCD (ICCD)
electron multiplying CCD (EMCCD)
electron bombardment CCD (EBCCD)
film
complementary metal oxide semiconductor (CMOS)
piezo-electric device
wide-field detection
narrow-field detection
absorption of illumination
inelastic scattering
elastic scattering
refractive index
optical path length gradient
retardance
stiffness
electron density
fluorescence emission
sub-nanosecond time-resolved fluorescence emission)
fluorescence polarization (polarization angle resolved fluorescence emission)
chemical composition
elevation
resolution-enhancing method
methods for increasing the resolution beyond the classical Abbe diffraction limit
optical method
computational method
in-focus phase contrast
defocus phase contrast
Wollaston prism
a birefringent optical element typically used to split polarized illumination into two sets of parallel but displaced rays
Hoffman modulation
single sideband edge enhancement (SSBE)
interference reflection contrast (IRM)
interference contrast
polarization contrast
structured illumination microscopy (SIM)
point-localization method
stimulated emission depletion (STED)
PALM (photoactivation localization microscopy)
STORM (stochastic optical reconstruction microscopy)
FIONA (fluorescence imaging with one nanometer accuracy)
DOPI (defocussed orientation and position imaging)
PAINT (point accumulation for imaging in nanoscale topography)
saturated structured-illumination microscopy (SSIM)
structured illumination used at sufficiently high power to cause significant ground-state depletion of the imaged fluorophore, thus allowing for non-linear resolution enhancement
UV/visible/IR illumination
X-ray illumination
microscopy with lenses
scanning probe microscopy
imaging by means of a physical probe that passes over the sample
mode of light microscopy
scanning tunneling microscopy
nearfield scanning optical microscopy (ANSOM)
ANSOM
Aperture-less NSOM.
polarized light illumination
orientation-independent polarization microscopy
polarization-sensitive detection
modified objective lens
Uses an objective with extra components to manipulate the wave front in the plane of the objective aperture.
linear method
a computational method that is linear in the mathematical sense, meaning that image intensity is conserved and the data remain suitable for all quantitative analyses
non-linear method
computational method that are mathematically non-linear; image intensity is not conserved, and the data are in general not suitable for quantitative analyses of pixel values
Wiener filter
3D-deconvolution
no-neighbors deblurring
nearest-neighbors deblurring
constrained iterative deconvolution
maximum likelihood deconvolution
blind deconvolution
exhaustive photon reassignment
light-sheet illumination
illumination in the form of a thin sheet of light directed perpendicular to the optic axis
FLIP
Fluorescence loss in photobleaching; a method of determining whether two populations of fluorophore are in diffusive communication with one another by observing the decrease in brightness of one population when the other population is subjected to continuous photobleaching.
FRAP
Fluorescence loss in photobleaching; a method of determining the rate and extent of exchange between a localized population of fluorophore and a non-localized diffusible pool, by observing the rate of recovery of brightness of the localized population after photobleaching.
FRET
Fluorescence (or Forster) resonance energy transfer; a method of estimating the distance between two fluorophores by measuring the extent of non-radiative energy transfer between the two. Experimentally, this involves selective excitation of one while observing emission from the other.
FLIM
SPIM
single (or selective) plane illumination.
CARS
coherent Raman anti-Stokes microscopy
OCT
optical coherence tomography; an interferometric method of imaging using back-scattered photons (elastic scattering)
secondary_electron imaging
image created using the electrons generated by ionization of a sample due to inelastic scattering of the primary beam of radiation
back-scattered_electron imaging
imaged formed using electrons undergoing elastic scattering at very high angles, with emission of characteristic X-rays
detection of photons
detection of electrons
detection of acoustic waves
detection of current induced in the specimen
UV/visible/IR photons
X-ray photons
scanning-transmission electron microscopy
EELS imaging
EFTEM energy filtered TEM
ESI electron spectroscopic imaging
EDAX imaging
specimen_modifying_illumination
Illumination used for the purpose of inducing some observable change in the specimen during the course of an imaging session. This illumination may or may not be the same as the illumination used for imaging. Typically used in conjunction with live-cell imaging
photo-bleaching illumination
photo-ablation illumination
photo-switching illumination
photo-activation illumination
uncaging illumination
trapping illumination
emission-depletion illumination
slit-scanning illumination
illumination in the shape of a thin line that is swept over the field of view
slit-scan confocal
illumination and detection via a thin slit
array-scan confocal
Fixed array of sources focused to an array of spots that is swept over the specimen in raster fashion
spot detector
area detector
visualization of contiguous regions
methods of visualization that differentiate between different regions or surfaces of the specimen based on contiguity
visualization by chemical attribute
methods of visualization that differentiate regions of the specimen on the basis of their chemical properties
shadowing and plating
visualization by depositing a label on the surface of a specimen uniformly (plating), or from a particular direction so that surface topography becomes visible (shadowing)
negative staining
visualization by exclusion of a stain in which the specimen is immersed; compare with "positive staining.
sequence-specific nucleic acid probe
antibody
lectin
small-molecule probe
fluorescent dextran fill
fluorescent protein tag
probes for nucleic acid
small genetically encoded tag
probe for protein
organelle-specific probe
macromolecular probe
probe for mitochondria
probe for endoplasmic reticulum
probe for Golgi
probe for lysosomes
stain with broad specificity
positive staining
tetracysteine tag
Hoechst 33258
genetically encoded biotin tag
freeze_fracture/freeze_etch
fluorescent protein derived from Aequorea victoria
membrane-permeant probe
membrane impermeant probe
acridine homodimer
7-amino-actinomycin D
conconavalin A
wheat germ agglutinin
Phaseolus vulgaris lectin PHA-L)
Arachis hypogaea (PNA)
Helix pomatia agglutinin
soybean agglutinin
cholera toxin B
peptide-nucleic acid probe
fluorescent protein derived from Anthozoa
optical highlighter
Blue fluorescent protein from Aequorea victoria
Cyan fluorescent protein from Aequorea
Green fluorescent protein from Aequorea
DiIC16
Yellow fluorescent protein from Aequorea
Alexa Fluor 488
Alexa Fluor 546
Alexa Fluor 568
Alexa Fluor 555
Alexa Fluor 594
Alexa Fluor 610
Alexa Fluor 633
Alexa Fluor 647
Fluorescein (FITC)
Rhodamine
TexasRed
fluorophore with ex/em 589/615
Tetramethyl rhodamine (TRITC)
fluorophore derivative of rhodamine with ex/em 547/572
fluorescent label
enzyme label
electron dense label
biotin
affinity for specific proteins
non-specific protein affinity
AzuriteFP
SiriusFP
non-immunological protein probe
alpha-bungarotoxin
botulinum toxin
tetrodotoxin
batrachatoxin
CeruleanFP
CyPet
SCFP
EmeraldFP
SuperfolderFP
T-SapphireFP
CitrineFP
SYFP
TopazFP
VenusFP
yPet
Blue fluorescent proteins from Anthozoa
Cyan fluorescent proteins from Anthozoa
Green fluorescent proteins from Anthozoa
Orange fluorescent proteins from Anthozoa
Red fluorescent proteins from Anthozoa
Far-red fluorescent proteins from Anthozoa
Yellow fluorescent proteins from Anthozoa
mTagBFP
AmCyanFP
mCyFP
mTFP1
TagCFP
AQ143
HcRed-tandemFP
KatushkaFP
mKateFP
mKate2FP
mPlumFP
tdKatuskaFP
tdRFP639
AceFP
Azami GreenFP
CopGFP
mWasabiFP
TagGFP
TagGFP2
ZsGreenFP
DsRed-ExpressFP
DsRed-Express2FP
DsRed-MaxFP
DsRed-monomerFP
DsRed2FP
dTomatoFP
Kusabira OrangeFP
Kusabira OrangeFP2
mOrangeFP
mOrange2FP
TagRFP
TagRFP-T
tdTomatoFP
turboRFP
AsRed2FP
eqFP611
HcRed1FP
JRedFP
mAppleFP
mCherryFP
mRasberryFP
mRFP1
mRubyFP
mStrawberryFP
tdRFP611
PhiYFP
TagYFP
TurboYFP
ZsYellowFP
fluorescent protein timer
photoactivatable fluorescent protein
photoconvertible fluorescent protein
photoconvertible/photoswitchable fluorescent protein
photoswitchable fluorescent protein
DsRed-ES FP
Fast-FT
Medium-FT
Slow-FT
PA-GFP
PA-CFP
PA-mCherry1FP
PA-mRFP
Phamret
Dendra2FP
dEOSFP
KaedeFP
mEOS2FP
mKikGR
wtEOSFP
wtKIikGR
IrisFP
bsDronpa
Dronpa
Dronpa-3
E2GFP
KFP1
mTFP0.7
PadronFP
rsCherryFP
rsCherryRevFP
rsFastLimeFP
optically-dense stain
electron-dense stain
uranyl salt
lead salt
osmium tetroxide
potassium permanganate
uranium compound
molybdenum compound
tungsten compound
aurothioglucose
other negative stain
other radioisotope
isolated subcellular component
A fragment of a cell, subcellular organelle, or macromolecular complex.
secondary electron generation
electrons generated by inelastic scattering of other radiation, the primary radiation.
critical_point dried specimen
specimen from which water has been removed by a process that avoids liquid-gas and solid-gas phase transitions.
unprocessed raw data
data as acquired, with no alterations that change the pixel values.
lyophilized specimen
specimen from which water has been removed by evaporation under vacuum at a temperature below freezing.
X-Rhodamine
fluorophore derivative of rhodamine with ex/em 580/605
serial block face SEM (SBFSEM)
A method of reconstructing 3D structure by combining serial sectioning with scanning EM.
elastic scattering of electrons
elastic scattering of photons
inelastic scattering of electrons
inelastic scattering of photons (Raman scattering)
source of contrast
The source of the variation in the imaged parameter across the field of view.
differences in chemical composition
distribution of epitope
form birefringence
intrinsic birefringence
stress-induced birefringence
distribution of a specific nucleic acid sequence
distribution of a specific protein
differences in adsorption or binding of stain
boundaries between regions with different refractive index
differences in amount of elastic light scattering
differences in deposition of metal shadow
differences in intrinsic optical density
fluorescence polarization microscopy
compartmentalization of stain or label
differences in fluorescence lifetime
differences in orientation of fluorophore
intrinsic mass distribution
X-ray fluorescence
heat fixed tissue
copper salt
dispersed cells in vitro
fluorescent protein derived from Arabidopsis
vidicon tube camera
phototropin 2
miniSOG
evanescent wave scattering
FTIR frustrated total internal reflection
evanescent wave microscopy
total internal reflection fluorescence TIRF
ground state depletion scanning (GSD)
freeze-substituted tissue
high-voltage electron microscopy (HVEM)
intermediate voltage electron microacopy (IVEM)
Biological Imaging Method