Volumetric data analysis enabled spatially resolved optoretinogram to measure the functional signals in the living retina

2021 ◽  
Author(s):  
Lijie Zhang ◽  
Rongyao Dong ◽  
Robert J. Zawadzki ◽  
Pengfei Zhang
Keyword(s):  
Data Analysis ◽  
Volumetric Data ◽  
Spatially Resolved

scholarly journals A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially resolved tissue phenotyping at single-cell resolution

2021 ◽  
Author(s):  
Michele Bortolomeazzi ◽  
Lucia Montorsi ◽  
Damjan Temelkovski ◽  
Mohamed Reda Keddar ◽  
Amelia Acha-Sagredo ◽  
...  
Keyword(s):  
Data Analysis ◽  
Single Cell ◽  
High Performance ◽  
Spatial Information ◽  
Single Cell Analysis ◽  
Biological Tissues ◽  
Imaging Data ◽  
Cell Identification ◽  
Spatially Resolved ◽  
Multiplexed Imaging

ABSTRACTMultiplexed imaging technologies enable to study biological tissues at single-cell resolution while preserving spatial information. Currently, the analysis of these data is technology-specific and requires multiple tools, restricting the scalability and reproducibility of results. Here we present SIMPLI (Single-cell Identification from MultiPlexed Images), a novel, technology-agnostic software that unifies all steps of multiplexed imaging data analysis. After processing raw images, SIMPLI performs a spatially resolved, single-cell analysis of the tissue as wells as cell-independent quantifications of marker expression to investigate features undetectable at the cell level. SIMPLI is highly customisable and can run on desktop computers as well as high-performance computing environments, enabling workflow parallelisation for the analysis of large datasets. It produces multiple outputs at each step, including tabular text files and visualisation plots. The containerised implementation and minimum configuration requirements make SIMPLI a portable and reproducible solution for multiplexed imaging data analysis. SIMPLI is available at: https://github.com/ciccalab/SIMPLI.

Electron Channeling Patterns

1977 ◽  
Vol 35 ◽  
pp. 12-13
Author(s):  
David C. Joy
Keyword(s):  
Electron Diffraction ◽  
Incidence Angle ◽  
Photographic Plate ◽  
Diffraction Effect ◽  
Angle Of Incidence ◽  
Bulk Single Crystal ◽  
Time Resolved ◽  
Electron Channeling ◽  
Spatially Resolved ◽  
Large Bulk

Electron channeling patterns (ECP) were first found by Coates (1967) while observing a large bulk, single crystal of silicon in a scanning electron microscope. The geometric pattern visible was shown to be produced as a result of the changes in the angle of incidence, between the beam and the specimen surface normal, which occur when the sample is examined at low magnification (Booker, Shaw, Whelan and Hirsch 1967).A conventional electron diffraction pattern consists of an angularly resolved intensity distribution in space which may be directly viewed on a fluorescent screen or recorded on a photographic plate. An ECP, on the other hand, is produced as the result of changes in the signal collected by a suitable electron detector as the incidence angle is varied. If an integrating detector is used, or if the beam traverses the surface at a fixed angle, then no channeling contrast will be observed. The ECP is thus a time resolved electron diffraction effect. It can therefore be related to spatially resolved diffraction phenomena by an application of the concepts of reciprocity (Cowley 1969).

Microchemical imaging in biomedical research

1992 ◽  
Vol 50 (2) ◽  
pp. 1118-1119
Author(s):  
P. Ingram
Keyword(s):  
Data Analysis ◽  
Electron Probe ◽  
The Other ◽  
X Ray ◽  
Cell Element ◽  
Physiological Information ◽  
Functional States ◽  
Elemental Maps ◽  
Electron Energy Loss ◽  
Secondary Ion

It is well established that unique physiological information can be obtained by rapidly freezing cells in various functional states and analyzing the cell element content and distribution by electron probe x-ray microanalysis. (The other techniques of microanalysis that are amenable to imaging, such as electron energy loss spectroscopy, secondary ion mass spectroscopy, particle induced x-ray emission etc., are not addressed in this tutorial.) However, the usual processes of data acquisition are labor intensive and lengthy, requiring that x-ray counts be collected from individually selected regions of each cell in question and that data analysis be performed subsequent to data collection. A judicious combination of quantitative elemental maps and static raster probes adds not only an additional overall perception of what is occurring during a particular biological manipulation or event, but substantially increases data productivity. Recent advances in microcomputer instrumentation and software have made readily feasible the acquisition and processing of digital quantitative x-ray maps of one to several cells.

FT-IR microspectroscopic analysis of diseased white matter brain tissues

1995 ◽  
Vol 53 ◽  
pp. 968-969
Author(s):  
Steven M. Le Vine ◽  
David L. Wetzel
Keyword(s):  
White Matter ◽  
Gray Matter ◽  
Twitcher Mouse ◽  
Grid Pattern ◽  
Marked Contrast ◽  
Spatially Resolved ◽  
Ft Ir ◽  
Ir Microspectroscopy ◽  
Chemical Evidence

In situ FT-IR microspectroscopy has allowed spatially resolved interrogation of different parts of brain tissue. In previous work the spectrrscopic features of normal barin tissue were characterized. The white matter, gray matter and basal ganglia were mapped from appropriate peak area measurements from spectra obtained in a grid pattern. Bands prevalent in white matter were mostly associated with the lipid. These included 2927 and 1469 cm-1 due to CH2 as well as carbonyl at 1740 cm-1. Also 1235 and 1085 cm-1 due to phospholipid and galactocerebroside, respectively (Figs 1and2). Localized chemical changes in the white matter as a result of white matter diseases have been studied. This involved the documentation of localized chemical evidence of demyelination in shiverer mice in which the spectra of white matter lacked the marked contrast between it and gray matter exhibited in the white matter of normal mice (Fig. 3).The twitcher mouse, a model of Krabbe’s desease, was also studied. The purpose in this case was to look for a localized build-up of psychosine in the white matter caused by deficiencies in the enzyme responsible for its breakdown under normal conditions.

Ultra-spatially resolved synchrotron powered FT-IR microspectroscopy of individual cells of biological material

1995 ◽  
Vol 53 ◽  
pp. 884-885
Author(s):  
David L. Wetzel ◽  
John A. Reffner ◽  
Gwyn P. Williams
Keyword(s):  
Thermal Noise ◽  
Spot Size ◽  
Acquisition Time ◽  
Thermal Source ◽  
Signal To Noise ◽  
Spatially Resolved ◽  
Good Spatial Resolution ◽  
Small Spot ◽  
Ft Ir ◽  
Ir Microspectroscopy

Synchrotron radiation is 100 to 1000 times brighter than a thermal source such as a globar. It is not accompanied with thermal noise and it is highly directional and nondivergent. For these reasons, it is well suited for ultra-spatially resolved FT-IR microspectroscopy. In efforts to attain good spatial resolution in FT-IR microspectroscopy with a thermal source, a considerable fraction of the infrared beam focused onto the specimen is lost when projected remote apertures are used to achieve a small spot size. This is the case because of divergence in the beam from that source. Also the brightness is limited and it is necessary to compromise on the signal-to-noise or to expect a long acquisition time from coadding many scans. A synchrotron powered FT-IR Microspectrometer does not suffer from this effect. Since most of the unaperatured beam’s energy makes it through even a 12 × 12 μm aperture, that is a starting place for aperture dimension reduction.

Spatially Resolved Photoelectron Spectroscopy: Recent Progress and Future Plans

1990 ◽  
Vol 48 (2) ◽  
pp. 388-389
Author(s):  
A. M. Bradshaw
Keyword(s):  
Photoelectron Spectroscopy ◽  
Chemical Reactivity ◽  
Target Material ◽  
Orbital Energy ◽  
Light Sources ◽  
Analytical Technique ◽  
Hartree Fock ◽  
Spatially Resolved ◽  
Koopmans Theorem ◽  
Surface Analytical Technique

X-ray photoelectron spectroscopy (XPS or ESCA) was not developed by Siegbahn and co-workers as a surface analytical technique, but rather as a general probe of electronic structure and chemical reactivity. The method is based on the phenomenon of photoionisation: The absorption of monochromatic radiation in the target material (free atoms, molecules, solids or liquids) causes electrons to be injected into the vacuum continuum. Pseudo-monochromatic laboratory light sources (e.g. AlKα) have mostly been used hitherto for this excitation; in recent years synchrotron radiation has become increasingly important. A kinetic energy analysis of the so-called photoelectrons gives rise to a spectrum which consists of a series of lines corresponding to each discrete core and valence level of the system. The measured binding energy, EB, given by EB = hv−EK, where EK is the kineticenergy relative to the vacuum level, may be equated with the orbital energy derived from a Hartree-Fock SCF calculation of the system under consideration (Koopmans theorem).

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