scholarly journals SIproc: an open-source biomedical data processing platform for large hyperspectral images

The Analyst ◽  
2017 ◽  
Vol 142 (8) ◽  
pp. 1350-1357 ◽  
Author(s):  
Sebastian Berisha ◽  
Shengyuan Chang ◽  
Sam Saki ◽  
Davar Daeinejad ◽  
Ziqi He ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Clinical Diagnosis ◽  
Vibrational Spectroscopy ◽  
Imaging Techniques ◽  
Spectroscopic Imaging ◽  
Hyperspectral Images ◽  
Biomedical Data ◽  
Significant Interest ◽  
Processing Platform

There has recently been significant interest within the vibrational spectroscopy community to apply quantitative spectroscopic imaging techniques to histology and clinical diagnosis.

Correct problem statements in biomedical data processing

1976 ◽  
Author(s):  
N. I. Moiseeva ◽  
M. Yu. Simonov ◽  
V. M. Sysuev
Keyword(s):  
Data Processing ◽  
Biomedical Data ◽  
Correct Problem

scholarly journals A Bimodal Fluorescence-Raman Probe for Cellular Imaging

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1699
Author(s):  
Jiarun Lin ◽  
Marcus E. Graziotto ◽  
Peter A. Lay ◽  
Elizabeth J. New
Keyword(s):  
Chemical Composition ◽  
Fluorescent Probes ◽  
Lipid Droplets ◽  
Imaging Techniques ◽  
Spectroscopic Imaging ◽  
Fluorescent Sensors ◽  
Chemical Environment ◽  
Novel Approach ◽  
Health And Disease ◽  
Raman Probe

Biochemical changes in specific organelles underpin cellular function, and studying these changes is crucial to understand health and disease. Fluorescent probes have become important biosensing and imaging tools as they can be targeted to specific organelles and can detect changes in their chemical environment. However, the sensing capacity of fluorescent probes is highly specific and is often limited to a single analyte of interest. A novel approach to imaging organelles is to combine fluorescent sensors with vibrational spectroscopic imaging techniques; the latter provides a comprehensive map of the relative biochemical distributions throughout the cell to gain a more complete picture of the biochemistry of organelles. We have developed NpCN1, a bimodal fluorescence-Raman probe targeted to the lipid droplets, incorporating a nitrile as a Raman tag. NpCN1 was successfully used to image lipid droplets in 3T3-L1 cells in both fluorescence and Raman modalities, reporting on the chemical composition and distribution of the lipid droplets in the cells.

scholarly journals Shock tube data processing tools using open source hardware and software platforms

2020 ◽  
Author(s):  
K. Thirumalesh ◽  
Salgeri Puttaswamy Raju ◽  
Hiriyur Mallaiah Somashekarappa ◽  
Kumaraswamy Swaroop
Keyword(s):  
Data Processing ◽  
Shock Tube ◽  
Open Source ◽  
Software Platforms ◽  
Open Source Hardware

scholarly journals Airborne Hyperspectral Data Acquisition and Processing in the Arctic: A Pilot Study Using the Hyspex Imaging Spectrometer for Wetland Mapping

2021 ◽  
Vol 13 (6) ◽  
pp. 1178
Author(s):  
Jordi Cristóbal ◽  
Patrick Graham ◽  
Anupma Prakash ◽  
Marcel Buchhorn ◽  
Rudi Gens ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Pilot Study ◽  
Data Processing ◽  
High Latitude ◽  
Hyperspectral Images ◽  
The Arctic ◽  
Wetland Mapping ◽  
Kappa Index ◽  
Spectral Angle Mapper ◽  
Spectral Angle

A pilot study for mapping the Arctic wetlands was conducted in the Yukon Flats National Wildlife Refuge (Refuge), Alaska. It included commissioning the HySpex VNIR-1800 and the HySpex SWIR-384 imaging spectrometers in a single-engine Found Bush Hawk aircraft, planning the flight times, direction, and speed to minimize the strong bidirectional reflectance distribution function (BRDF) effects present at high latitudes and establishing improved data processing workflows for the high-latitude environments. Hyperspectral images were acquired on two clear-sky days in early September, 2018, over three pilot study areas that together represented a wide variety of vegetation and wetland environments. Steps to further minimize BRDF effects and achieve a higher geometric accuracy were added to adapt and improve the Hyspex data processing workflow, developed by the German Aerospace Center (DLR), for high-latitude environments. One-meter spatial resolution hyperspectral images, that included a subset of only 120 selected spectral bands, were used for wetland mapping. A six-category legend was established based on previous U.S. Geological Survey (USGS) and U.S. Fish and Wildlife Service (USFWS) information and maps, and three different classification methods—hybrid classification, spectral angle mapper, and maximum likelihood—were used at two selected sites. The best classification performance occurred when using the maximum likelihood classifier with an averaged Kappa index of 0.95; followed by the spectral angle mapper (SAM) classifier with a Kappa index of 0.62; and, lastly, by the hybrid classifier showing lower performance with a Kappa index of 0.51. Recommendations for improvements of future work include the concurrent acquisition of LiDAR or RGB photo-derived digital surface models as well as detailed spectra collection for Alaska wetland cover to improve classification efforts.

scholarly journals A python code for automatic construction of Fischer plots using proxy data

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daming Yang ◽  
Yongjian Huang ◽  
Zongyang Chen ◽  
Qinghua Huang ◽  
Yanguang Ren ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Lake Level ◽  
Gamma Ray ◽  
Data Series ◽  
Proxy Data ◽  
Cycle Number ◽  
Automatic Construction ◽  
Natural Gamma ◽  
Graphic Representations

AbstractFischer plots are widely used in paleoenvironmental research as graphic representations of sea- and lake-level changes through mapping linearly corrected variation of accumulative cycle thickness over cycle number or stratum depth. Some kinds of paleoenvironmental proxy data (especially subsurface data, such as natural gamma-ray logging data), which preserve continuous cyclic signals and have been largely collected, are potential materials for constructing Fischer Plots. However, it is laborious to count the cycles preserved in these proxy data manually and map Fischer plots with these cycles. In this paper, we introduce an original open-source Python code “PyFISCHERPLOT” for constructing Fischer Plots in batches utilizing paleoenvironmental proxy data series. The principle of constructing Fischer plots based on proxy data, the data processing and usage of the PyFISCHERPLOT code and the application cases of the code are presented. The code is compared with existing methods for constructing Fischer plots.

Electron spectroscopic imaging of the centrosome in cells of the Indian muntjac

1988 ◽  
Vol 91 (1) ◽  
pp. 5-11
Author(s):  
J.B. Rattner ◽  
D.P. Bazett-Jones
Keyword(s):  
Imaging Techniques ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Intact Cells ◽  
Thin Sections ◽  
Indian Muntjac ◽  
Phosphorylated Proteins ◽  
Linking Elements ◽  
The Matrix ◽  
Precise Distribution

Specific antibody labelling indicates that phosphoproteins are present at microtubule-organizing centres, including the centrosome. We have employed electron spectroscopic imaging techniques that permit high-resolution elemental analysis of thin sections of intact cells to investigate the precise distribution of phosphorus and therefore phosphoproteins at the centrosome of Indian muntjac cells. We report that these proteins are localized to both the pericentriolar matrix and the centriole. The matrix contains an abundance of phosphorus and is associated with microtubule elements. Within the mature centriole, major structures including the nine triplet blades and linking elements that connect adjacent blades are composed of phosphorylated proteins. In addition, phosphoproteins are abundant at the ends of the centriole, at the interface between the centriole lumen and the pericentriolar environment. From these observations we suggest that phosphoproteins may play both a structural and a functional role within the centrosome region.

scholarly journals Medical Informatics in Morocco: Casablanca Medical Informatics Laboratory

2007 ◽  
Vol 16 (01) ◽  
pp. 138-140
Author(s):  
S. Diouny ◽  
K. Balar ◽  
M. Bennani Othmani
Keyword(s):  
Data Processing ◽  
Medical Informatics ◽  
New Technologies ◽  
Research Unit ◽  
Processing Unit ◽  
Biomedical Data ◽  
Professional Activities ◽  
Research Activities ◽  
Medical Data Processing ◽  
International Projects

SummaryIn 2005, Medical Informatics Laboratory (CMIL) became an independent research unit within the Faculty of Medicine and Pharmacy of Casablanca. CMIL is currently run by three persons (a university professor, a data processing specialist and a pedagogical assistant). The objectives of CMIL are to promote research and develop quality in the field of biomedical data processing and health, and integrate new technologies into medical education and biostatistics. It has four units: Telehealth Unit, Network Unit, Biostatistics Unit, Medical data processing Unit.The present article seeks to give a comprehensive account of Casablanca Medical informatics laboratory (CMIL) activities. For ease of exposition, the article consists of four sections: Section I discusses the background of CMIL; section II is devoted to educational activities; section III addresses professional activities; and section IV lists projects that CMIL is involved in.Since its creation, CMIL has been involved in a number of national and international projects, which have a bearing on Telemedicine applications, E-learning skills and data management in medical studies in Morocco.It is our belief that the skills and knowledge gained in the past few years would certainly enrich our research activities, and improve the situation of research in Medical informatics in Morocco.

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