Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Optical mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources
PubMed1988

Retinotopic refinement of the regenerating goldfish optic tract is not linked to activity-dependent refinement of the retinotectal map.

The cut optic nerve of a goldfish can regenerate, restoring an orderly projection from the retina to the optic tectum. At first, regenerating axons make transient connections, many of them in inappropriate tectal locations. Later, their arrangement is gradually refined into an accurate retinotectal map by a process that depends on afferent activity. On their way to the tectum, many regenerating axons make erroneous choices between the two arms (brachia) of the optic tract. However, since they commonly possess divergent collateral branches, a secondary refinement of the brachial pattern can occur by selective collateral elimination. How or why a particular collateral is lost is not known, but we have previously suggested that sibling branches might compete to form stable tectal synapses, implying that there might be a causal link between refinement of the brachial pattern and refinement of the retinotectal map. In this paper, we have tested directly for such a link, blocking map refinement with tetrodotoxin (TTX) or stroboscopic light, verifying the effectiveness of the block and measuring the extent of brachial refinement by standard methods in experimental and control fish. Both TTX and stroboscopic light reliably prevented map refinement, their results being indistinguishable. However, neither had even the slightest detrimental effect on brachial refinement, either 42 days or 70 days after nerve cut. Evidently, neither activity nor a sharp retinotectal projection is necessary for brachial refinement. Theory and experiment both dictate that the basic projection pattern be controlled by a mechanism (such as chemoaffinity) that is independent of activity, and it would seem that selective collateral loss must depend on the same mechanism.

Animals↗
PubMed2006

Broadband ultrasound field mapping system using a wavelength tuned, optically scanned focused laser beam to address a Fabry Perot polymer film sensor.

An optical system for rapidly mapping broad-band ultrasound fields with high spatial resolution has been developed. The transduction mechanism is based upon the detection of acoustically induced changes in the optical thickness of a thin polymer film acting as a Fabry Perot sensing interferometer (FPI). By using a PC-controlled galvanometer mirror to line-scan a focused laser beam over the surface of the FPI, and a wavelength-tuned phase bias control system to optimally set the FPI working point, a notional 1D ultrasound array was synthesized. This system enabled ultrasound fields to be mapped over an aperture of 40 mm, in 50-microm steps with an optically defined element size of 50 microm and an acquisition time of 50 ms per step. The sensor comprised a 38-microm polymer film FPI which was directly vacuum-deposited onto an impedance-matched polycarbonate backing stub. The -3 dB acoustic bandwidth of the sensor was 300 kHz to 28 MHz and the peak noise-equivalent-pressure was 10 kPa over a 20-MHz measurement bandwidth. To demonstrate the system, the outputs of various planar and focused pulsed ultrasound transducers with operating frequencies in the range 3.5 to 20 MHz were mapped. It is considered that this approach offers a practical and inexpensive alternative to piezoelectric-based arrays and scanning systems for rapid transducer field characterization and biomedical and industrial ultrasonic imaging applications.

Journal Article↗
PubMed2001

Fiber-optic fluorometer for microscale mapping of photosynthetic pigments in microbial communities.

Microscale fluorescence measurements were performed in photosynthetic biofilms at a spatial resolution of 100 to 200 microm with a new fiber-optic fluorometer which allowed four different excitation and emission wavelengths and was configured for measuring phycobiliproteins, chlorophylls, and bacteriochlorophylls. We present details of the measuring system and describe examples of applications in different microbial communities.

Bacterial Proteins↗
PubMed2004

Functional magnetic resonance imaging and optical imaging for dominant-hemisphere perisylvian arteriovenous malformations.

OBJECTIVE: In this study, we developed an a priori system to stratify surgical intervention of perisylvian arteriovenous malformations (AVMs) in 20 patients. We stratified the patients into three categories based on preoperative functional magnetic resonance imaging (fMRI) language activation pattern and relative location of the AVM. METHODS: In Group I (minimal risk), the AVM was at least one gyrus removed from language activation, and patients subsequently underwent asleep resection. In Group II (high risk), the AVM and language activation were intimately associated. Because the risk of postoperative language deficit was high, these patients were then referred to radiosurgery. In Group III (indeterminate risk), the AVM and language were adjacent to each other. The risk of language deficit could not be predicted on the basis of the fMRI alone. These patients underwent awake craniotomy with electrocortical stimulation mapping and optical imaging of intrinsic signals for language mapping. RESULTS: All patients from Group I (minimal risk) underwent asleep resection without deficit. All Group II (high-risk) patients tolerated radiosurgery without complication. In Group III (indeterminate risk), three patients underwent successful resection, whereas two underwent aborted resection after intracranial mapping. CONCLUSION: We advocate the use of fMRI to assist in the preoperative determination of operability by asleep versus awake craniotomy versus radiosurgery referral. In addition, we advocate the use of all three functional mapping (fMRI, electrocortical stimulation mapping, and optical imaging of intrinsic signals) techniques to clarify the eloquence score of the Spetzler-Martin system before definitive treatment (anesthetized resection versus radiosurgery versus intraoperative resection versus intraoperative closure and radiosurgery referral).

Adult↗
PubMed2003

Intraocular lens calculations in patients with corneal scarring and irregular astigmatism.

PURPOSE: To compare various methods of estimating corneal power for intraocular lens (IOL) calculation in patients with irregular corneal astigmatism. SETTING: Pepose Vision Institute, St. Louis, Missouri, USA. Case reports and review of the medical literature. RESULTS: Two patients with irregular corneal astigmatism had an IOL exchange after a "surprise" post-cataract-surgery refraction. In the first case, the patient had a post-cataract-surgery refraction of +5.50 -0.75 x 69 and in the second case, a refraction of -7.00 -1.00 x 180. The central corneal power before IOL exchange was assessed using manual keratometry, various computerized videokeratography curvature and power maps, and contact lens overrefraction. The total axial power map (Orbscan(R), Bausch & Lomb), total optical power map (Orbscan), and contact lens overrefraction method provided the most accurate estimates of central corneal power in these 2 patients. CONCLUSION: Computerized scanning-slit videokeratography, which analyzes the anterior and posterior surfaces of the cornea, and the contact lens overrefraction method gave good estimations of corneal power in patients with irregular corneal astigmatism. This type of analysis may improve the accuracy of IOL calculation in patients with corneal pathology and irregular astigmatism.

Adult↗
PubMed2002

Color processing in macaque striate cortex: relationships to ocular dominance, cytochrome oxidase, and orientation.

We located clusters of color-selective neurons in macaque striate cortex, as mapped with optical imaging and confirmed with electrophysiological recordings. By comparing responses to an equiluminant red/green stimulus versus a high-contrast luminance stimulus, we were able to reveal a patchy distribution of color selectivity. Other color imaging protocols, when compared with electrophysiological data, did not reliably indicate the location of functional structures. The imaged color patches were compared with other known functional subdivisions of striate cortex. There was a high degree of overlap of the color patches with the cytochrome-oxidase (CO) blobs. The patches were often larger than a single blob in size, however, and in some instances spanned two neighboring blobs. More than one-half (56%) of the color-selective patches seen in optical imaging were not confined to one ocular dominance (OD) column. Almost one-quarter of color patches (23%) extended across OD columns to encompass two blobs of different eye preference. We also compared optical images of orientation selectivity to maps of color selectivity. Results indicate that the layout of orientation and color selectivity are not directly related. Specifically, despite having similar scales and distributions, the maps of orientation and color selectivity were not in consistent alignment or registration. Further, we find that the maps of color selectivity and of orientation are each only loosely related to maps of OD. This description stands in contrast to a common depiction of color-selective regions as identical to CO blobs, appearing as pegs in the centers of OD columns in the classical "ice cube" model. These results concerning the pattern of color selectivity in V1 support the view (put forth in previous imaging studies of the organization of orientation and ocular dominance) that there is not a fundamental registration of functional hypercolumns in V1.

Animals↗
PubMed2000

Complex optical constants on a subwavelength scale.

Optical phase contrast has for the first time been observed on a nanometer scale, with a near-field microscope of scattering type that maps the complete optical field of amplitude and phase. Backed by quasielectrostatic theory, we demonstrate the significance and experimental accessibility of even complex optical constants on a subwavelength scale. Further, our method can separate the near-field response from background artifacts and thus is expected to enable nanoscale optical mapping of even topography-rich objects such as resonant clusters and macromolecules.

Journal Article↗
PubMed2006

High-resolution mapping of quantum efficiency of silicon photodiode via optical-feedback laser microthermography.

We map the external quantum efficiency (QE) distribution of a silicon photodiode (PD) sample via a thermographic imaging technique based on optical-feedback laser confocal microscopy. An image pair consisting of the confocal reflectance image and the 2D photocurrent map is simultaneously acquired to delineate the following regions of interest on the sample: the substrate, the n-type region, the pn overlay, and the bonding pad. The 2D QE distribution is derived from the photocurrent map to quantify the optical performance of these sites. The thermal integrity of the sample is then evaluated by deriving the rate of change of QE with temperature T at each point on the silicon PD. These gradient maps function not only as stringent measures of local thermal QE activity but they also expose probable defect locations on the sample at high spatial resolution--a capability that is not feasible with existing bulk measurement techniques.

Journal Article↗
PubMed2006

Detection of glaucomatous optic nerve head by using Heidelberg topographic maps.

PURPOSE: To evaluate the capacity of a new topographic map analysis to detect abnormal optic discs from healthy ones in a new cohort of subjects. PATIENTS AND METHODS: Only one eye was chosen randomly from each subject included in the study. In total, 20 normal eyes with a normal visual field, an IOP of <22 mmHg and no history of glaucoma in their family, and 20 glaucomatous eyes with an abnormal visual field and an open angle were selected. All the subjects were examined with the Heidelberg Retina Tomograph (HRT, Heidelberg Engineering GMBH, Heidelberg, Germany) and Humphrey Perimeter, program 30-2 (Humphrey Instrument, Inc., San Leandro, CA, USA). Topographic maps analysis was performed to each HRT optic nerve head image. Sensitivity, specificity, and diagnostic precision were calculated. RESULTS: When the topographic map analysis was applied to the group, a sensitivity of 80%, a specificity of 75%, and a diagnostic precision of 77.5% were obtained. CONCLUSION: Using the topographic map analysis, the HRT capacity to differentiate normal optic discs from those with glaucoma was similar to those already published in the literature, but using this technique there is no input from the observer to draw the contourline and reference plane is not necessary.

Aged↗
PubMed1996

Identification of seven new human MHC class I region genes around the HLA-F locus.

Using cDNA hybridization selection techniques, we identified seven new genes in a 280 kilobase YAC covering the HLA-F locus. The new genes were mapped back to the YAC by a combination of optical restriction mapping and pulse field gel electrophoresis. Northern analysis of individual clones demonstrated the presence of either different mRNA sizes or different expression patterns. Two of the cDNA clones were expressed only in lymphoid cell lines: one in Jurkat cells (T cell) and another in JY cells (B cell). All the genes lacked sequence similarity to any known classical and non-classical major histocompatibility complex (MHC) class I genes, indicating that the MHC class I region has more functions than anticipated. Of the seven new genes, one is highly similar (97%) to mouse 60S ribosomal protein, and another is homologous to diubiquitin proteins. Of the two G-coupled receptor-like cDNAs, one was fully sequenced and found to be an olfactory receptor-like gene. The study strengthens evidence that the MHC complex not only plays a key role in the immune system, but also contributes to non-immunological functions.

Animals↗
PubMed1998

Comparison of finite-difference transport and diffusion calculations for photon migration in homogeneous and heterogeneous tissues.

We analyse the limits of the diffusion approximation to the time-independent equation of radiative transfer for homogeneous and heterogeneous biological media. Analytical calculations and finite-difference simulations based on diffusion theory are compared with discrete-ordinate, finite-difference transport calculations. The influence of the ratio of absorption and transport scattering coefficient (mu(a)/mu'(s)) on the accuracy of the diffusion approximation are quantified and different definitions for the diffusion coefficient, D, are discussed. We also address effects caused by void-like heterogeneities in which absorption and scattering are very small compared with the surrounding medium. Based on results for simple homogeneous and heterogeneous systems, we analyse diffusion and transport calculation of light propagation in the human brain. For these simulations we convert density maps obtained from magnetic resonance imaging (MRI) to optical-parameter maps (mu(a) and mu'(s)) of the brain. We show that diffusion theory fails to describe accurately light propagation in highly absorbing regions, such as haematoma, and void-like spaces, such as the ventricles and the subarachnoid space.

Absorption↗
PubMed2000

Solh, the mouse homologue of the Drosophila melanogaster small optic lobes gene: organization, chromosomal mapping, and localization of gene product to the olfactory bulb.

The Drosophila melanogaster small optic lobes gene (sol) is required for normal development of the neuropiles of the medulla and lobula complexes of the adult optic lobes. The predicted protein products of sol and its human homologue SOLH contain zinc-finger-like repeats, a calpain-like protease domain, and a C-terminal domain of unknown function. Long-distance PCR was used to amplify genomic DNA for Solh, the mouse homologue of sol, following the identification of mouse Solh expressed sequence tags. The nucleotide sequence of the Solh coding region (6.0 kb) was determined. The predicted Solh protein of 1095 amino acid residues shows 89% identity (93% similarity) to the human homologue. Solh was localized by in situ hybridization to band A3.3 on mouse Chromosome 17, in a region of maintained homology with human 16p13.3. Antipeptide antibodies were prepared and verified by demonstration of specific reactivity with recombinant human SOLH protein prepared by in vitro transcription/translation and expression in insect cells using the baculovirus system. The antibodies were used to show that the Solh protein localizes to the olfactory bulb in mouse and rat brain, suggesting that it could have an analogous role in development of sensory system neurons in Drosophila and in mammals.

Amino Acid Sequence↗
PubMed1998

Optical time-of-flight chemical detection: spatially resolved analyte mapping with extended-length continuous chemically modified optical fibers.

We theoretically evaluate and experimentally verify a novel strategy for spatially resolved analyte mapping over extended remote areas. The approach combines a method for the fabrication of continuous extended-length sensors with optical time-of-flight chemical detection (OTOF-CD). The use of OTOF-CD makes it possible to locate the zones in the fiber where attenuation or fluorescence takes place, to determine the magnitude of these variations, and to relate the magnitude of the variations to the local concentration or concentrations of a single analyte or several analytes. Simulation experiments suggest that OTOF-CD should provide spatial resolution close to its theoretical limit by deconvolution of the returned wave form with all time-dependent experimental variables (laser pulse width, reagent fluorescence lifetime, etc.). The signal-processing technique should be useful for a wide variety of sensors based on absorption, refractive index, or statically and dynamically quenched fluorescence. Experimental results with a model system (a 48-m-long oxygen sensor) compare favorably with those predicted by numerical simulations. Possible experimental difficulties in the realization of these novel sensors are discussed as are ways to overcome them.

Adsorption↗
PubMed2005

Electrically conductive and optically transparent Sb-doped SnO2 STM-probe for local excitation of electroluminescence.

We demonstrate that an optically transparent and electrically conductive antimon-doped tin-oxide tip that is prepared in a sol-gel process can be used as a probe for scanning tunnelling microscopy (STM), yielding atomic vertical and nanometre lateral resolution. Emission of visible light from the tunnelling junction between gold particles and the tip is observed for bias voltages above 7 V. In contrast to the metallic tips generally used in STM, this tip does not significantly perturb the local optical response. Therefore, the tunnelling induced light can be used to map the optical near-field of surface structures with the tunnel gap acting as highly localised light source for the investigation of near-field enhancement in complex metal structures.

Journal Article↗
PubMed1988

Early blindness results in a degraded auditory map of space in the optic tectum of the barn owl.

The optic tectum of the barn owl (Tyto alba) contains a neural map of auditory space consisting of neurons that are sharply tuned for sound source location and organized precisely according to their spatial tuning. The importance of vision for the development of this auditory map was investigated by comparing space maps measured in normal owls with those measured in owls raised with both eyelids sutured closed. The results demonstrate that owls raised without sight, but with normal hearing, develop auditory space maps with degraded precision and with aspects of topography that are abnormal.

Animals↗