Methods for Hyperspectral Microscope Calibration and Spectra Normalization from Images of Bacteria Cells

2018 ◽  
Vol 61 (2) ◽  
pp. 438-448 ◽  
Author(s):  
Matthew B. Eady ◽  
Bosoon Park ◽  
Seung-Chul Yoon ◽  
Mark A. Haidekker ◽  
Kurt C. Lawrence
Keyword(s):  
Single Cell ◽  
Spectral Data ◽  
Light Source ◽  
Exposure Time ◽  
Scatter Correction ◽  
Peak Shift ◽  
Cellular Level ◽  
Tunable Filter ◽  
Radiometric Calibration ◽  
Halogen Light

Abstract. Hyperspectral microscope images (HMIs) have previously shown promise as a means for rapid and early detection of foodborne bacteria at the cellular level. System calibration and data normalization are critical for comparing information obtained from HMIs collected with multiple instruments and system parameters. Here, we implement a wavelength and radiometric calibration for spectral data obtained from a hyperspectral microscope, assess the spatial uniformity of HMIs, and show the need to normalize data from single-cell regions of interest (ROIs). A hyperspectral microscope with a tungsten halogen light source, acousto-optical tunable filter, and electron multiplying camera with variable gain and exposure time settings were used. HMIs were collected at additional gain settings of 0%, 1.6%, 3.5%, and 5.1% along with ten exposure time settings between 100 and 1000 ms with both calibration lamps. Wavelength peak shift started to occur at an exposure time of 600 ms for 1.6% gain, at 400 ms for 3.5% gain, and at 200 ms for 5.1% gain. HMIs of , Typhimurium, and cells were collected to assess spectral data normalcy and the need for preprocessing spectra from single bacteria cells. Spatial characteristics of cells were assessed by HMIs of a glass slide with a micrometer for determining pixel size from the field of view. HMIs were preprocessed by normalizing cell spectra to the light source and applying multiplicative scatter correction. Data normalcy was assessed on both the raw and preprocessed data sets. Preprocessing the data was found to reduce the cell-to-cell variation associated with a single-cell ROI method, while outliers were detected and verified through HMIs as physically different from other cells. Keywords: Bacteria, Calibration, Food safety, Hyperspectral microscope, Pathogen.

scholarly journals Effects of Light Curing Method and Exposure Time on Mechanical Properties of Resin Based Dental Materials

2008 ◽  
Vol 02 (01) ◽  
pp. 37-42 ◽  
Author(s):  
A. Rıza Alpöz ◽  
Fahinur Ertuḡrul ◽  
Dilsah Cogulu ◽  
Aslı Topaloḡlu Ak ◽  
Metin Tanoḡlu ◽  
...  
Keyword(s):  
Compressive Strength ◽  
Light Source ◽  
Exposure Time ◽  
Resin Composite ◽  
Dental Materials ◽  
Glass Ionomer Cement ◽  
Curing Time ◽  
Uniform Size ◽  
Halogen Light ◽  
Light Curing

ABSTRACTObjectives: The aim of this study was to investigate microhardness and compressive strength of composite resin (Tetric-Ceram, Ivoclar Vivadent), compomer (Compoglass, Ivoclar, Vivadent), and resin modified glass ionomer cement (Fuji II LC, GC Corp) polymerized using halogen light (Optilux 501, Demetron, Kerr) and LED (Bluephase C5, Ivoclar Vivadent) for different curing times.Methods: Samples were placed in disc shaped plastic molds with uniform size of 5 mm diameter and 2 mm in thickness for surface microhardness test and placed in a diameter of 4 mm and a length of 2 mm teflon cylinders for compressive strength test. For each subgroup, 20 samples for microhardness (n=180) and 5 samples for compressive strength were prepared (n=45). In group 1, samples were polymerized using halogen light source for 40 seconds; in group 2 and 3 samples were polymerized using LED light source for 20 seconds and 40 seconds respectively. All data were analyzed by two way analysis of ANOVA and Tukey’s post-hoc tests.Results: Same exposure time of 40 seconds with a low intensity LED was found similar or more efficient than a high intensity halogen light unit (P>.05), however application of LED for 20 seconds was found less efficient than 40 seconds curing time (P=.03).Conclusions: It is important to increase the light curing time and use appropriate light curing devices to polymerize resin composite in deep cavities to maximize the hardness and compressive strength of restorative materials. (Eur J Dent 2008;2:37-42)

Comparison of the effects of operating microscopes with light emitting diode and halogen light source on the eye: a rabbit study

2021 ◽  
pp. 1-7
Author(s):  
Bahri Aydın ◽  
Armagan Ozgur ◽  
Huseyin Baran Ozdemir ◽  
Pınar Uyar Gocun ◽  
Mehmet Arda Inan ◽  
...  
Keyword(s):  
Light Source ◽  
Light Emitting Diode ◽  
Light Emitting ◽  
Halogen Light ◽  
Halogen Light Source

Absolute Radiometric Calibration of the VIIRS DNB HGS with the Ground Based Automated Accurate Active Light Source (AALS): Early Results

2018 ◽  
Author(s):  
Robert Ryan ◽  
Mary Pagnutti ◽  
Timothy Ruggles ◽  
Kara Burch ◽  
Larry Leigh ◽  
...  
Keyword(s):  
Light Source ◽  
Radiometric Calibration ◽  
Early Results

Comparison of Composite Curing Parameters: Effects of Light Source and Curing Mode on Conversion, Temperature Rise and Polymerization Shrinkage

10.2341/05-15 ◽  
2006 ◽  
Vol 31 (2) ◽  
pp. 219-226 ◽  
Author(s):  
Z. Tarle ◽  
A. Knezevic ◽  
N. Demoli ◽  
A. Meniga ◽  
J. Sutalo ◽  
...  
Keyword(s):  
Light Source ◽  
Temperature Rise ◽  
Thermal Injury ◽  
Resin Composite ◽  
Marginal Adaptation ◽  
Low Intensity ◽  
Halogen Light ◽  
Lower Temperature ◽  
Final Degree ◽  
Conversion Temperature

Clinical Relevance The use of a low intensity light source for photopolymerization based on LED technology provides equivalent final degree conversion with possible flow of the resin composite, similar to when QTH technology is used. At the same time, the lower temperature rise in the sample and the more favorable development of shrinkage kinetics compared to the higher intensities of halogen light may aid in maintaining marginal adaptation while avoiding possible thermal injury.

scholarly journals A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics

2021 ◽  
Author(s):  
Joseph Burclaff ◽  
R. Jarrett Bliton ◽  
Keith A Breau ◽  
Meryem T Ok ◽  
Ismael Gomez-Martinez ◽  
...  
Keyword(s):  
Small Intestine ◽  
Single Cell ◽  
Drug Targets ◽  
Healthy Adult ◽  
Cellular Level ◽  
Cell Junction ◽  
Marker Genes ◽  
Human Small Intestine ◽  
Adult Human ◽  
Human Intestinal Epithelium

Background and Aims: Single-cell transcriptomics offer unprecedented resolution of tissue function at the cellular level, yet studies in healthy adult human small intestine and colon are sparse. Here, we present single-cell transcriptomics from 3 humans covering the duodenum, jejunum, ileum, and ascending, transverse, and descending colon. Methods: 12,590 single epithelial cells from three independently processed organ donors were evaluated for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. Analyses focused on intrinsic cell properties and capacity for response to extrinsic signals along the gut axis across different humans. Results: Cells were assigned to 25 epithelial lineage clusters. Human intestinal stem cells (ISCs) are not specifically marked by many murine ISC markers. Lysozyme expression is not unique to Paneth cells (PCs), and PCs lack expression of expected niche-factors. BEST4 cells express NPY and show functional and maturational differences between SI and colon. Tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors. Some classes of mucins, hormones, cell-junction, and nutrient absorption genes show unappreciated regional expression differences across lineages. Differential expression of receptors and drug targets across lineages reveals biological variation and potential for variegated responses. Conclusions: Our study identifies novel lineage marker genes; covers regional differences; shows important differences between mouse and human gut epithelium; and reveals insight into how the epithelium responds to the environment and drugs. This comprehensive cell atlas of the healthy adult human intestinal epithelium resolves data gaps in anatomical regions along the gastrointestinal tract and advances our understanding of human intestinal physiology.

scholarly journals Nondestructive Testing and Visualization of Catechin Content in Black Tea Fermentation Using Hyperspectral Imaging

Sensors ◽  
2021 ◽  
Vol 21 (23) ◽  
pp. 8051
Author(s):  
Chunwang Dong ◽  
Chongshan Yang ◽  
Zhongyuan Liu ◽  
Rentian Zhang ◽  
Peng Yan ◽  
...  
Keyword(s):  
Spectral Data ◽  
Prediction Accuracy ◽  
Visual Analysis ◽  
Population Analysis ◽  
Scatter Correction ◽  
Principal Component ◽  
Black Tea ◽  
Support Vector ◽  
Epicatechin Gallate ◽  
Variable Combination

Catechin is a major reactive substance involved in black tea fermentation. It has a determinant effect on the final quality and taste of made teas. In this study, we applied hyperspectral technology with the chemometrics method and used different pretreatment and variable filtering algorithms to reduce noise interference. After reduction of the spectral data dimensions by principal component analysis (PCA), an optimal prediction model for catechin content was constructed, followed by visual analysis of catechin content when fermenting leaves for different periods of time. The results showed that zero mean normalization (Z-score), multiplicative scatter correction (MSC), and standard normal variate (SNV) can effectively improve model accuracy; while the shuffled frog leaping algorithm (SFLA), the variable combination population analysis genetic algorithm (VCPA-GA), and variable combination population analysis iteratively retaining informative variables (VCPA-IRIV) can significantly reduce spectral data and enhance the calculation speed of the model. We found that nonlinear models performed better than linear ones. The prediction accuracy for the total amount of catechins and for epicatechin gallate (ECG) of the extreme learning machine (ELM), based on optimal variables, reached 0.989 and 0.994, respectively, and the prediction accuracy for EGC, C, EC, and EGCG of the content support vector regression (SVR) models reached 0.972, 0.993, 0.990, and 0.994, respectively. The optimal model offers accurate prediction, and visual analysis can determine the distribution of the catechin content when fermenting leaves for different fermentation periods. The findings provide significant reference material for intelligent digital assessment of black tea during processing.

scholarly journals Convergence of oncogenic cooperation at single-cell and single-gene levels drives leukemic transformation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yuxuan Liu ◽  
Zhimin Gu ◽  
Hui Cao ◽  
Pranita Kaphle ◽  
Junhua Lyu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cancer Progression ◽  
Single Gene ◽  
Myeloid Cell ◽  
Cellular Level ◽  
Integrative Approach ◽  
Cancer Evolution ◽  
Cell Assays

AbstractCancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. Using a mouse model harboring NRasG12D and EZH2 mutations that recapitulates leukemic progression, we employ single-cell transcriptomic profiling to map cellular composition and gene expression alterations in healthy or diseased bone marrows during leukemogenesis. At cellular level, NRasG12D induces myeloid lineage-biased differentiation and EZH2-deficiency impairs myeloid cell maturation, whereas they cooperate to promote myeloid neoplasms with dysregulated transcriptional programs. At gene level, NRasG12D and EZH2-deficiency independently and synergistically deregulate gene expression. We integrate results from histopathology, leukemia repopulation, and leukemia-initiating cell assays to validate transcriptome-based cellular profiles. We use this resource to relate developmental hierarchies to leukemia phenotypes, evaluate oncogenic cooperation at single-cell and single-gene levels, and identify GEM as a regulator of leukemia-initiating cells. Our studies establish an integrative approach to deconvolute cancer evolution at single-cell resolution in vivo.

A single cell approach to problems of cell lineage and commitment during embryogenesis of Drosophila melanogaster

Development ◽  
1987 ◽  
Vol 100 (1) ◽  
pp. 1-12 ◽  
Author(s):  
G.M. Technau
Keyword(s):  
Drosophila Melanogaster ◽  
Single Cell ◽  
Cell Lineage ◽  
Cellular Level ◽  
Central Importance ◽  
Cell Level ◽  
Combined Application ◽  
A Cell ◽  
Pole Cells ◽  
Drosophila Embryos

The mechanisms leading to the commitment of a cell to a particular fate or to restrictions in its developmental potencies represent a problem of central importance in developmental biology. Both at the genetic and at the molecular level, studies addressing this topic using the fruitfly Drosophila melanogaster have advanced substantially, whereas, at the cellular level, experimental techniques have been most successfully applied to organisms composed of relatively large and accessible cells. The combined application of the different approaches to one system should improve our understanding of the process of commitment as a whole. Recently, a method has been devised to study cell lineage in Drosophila embryos at the single cell level. This method has been used to analyse the lineages, as well as the state of commitment of single cell progenitors from various ectodermal, mesodermal and endodermal anlagen and of the pole cells. The results obtained from a clonal analysis of wild-type larval structures are discussed in this review.

EVALUATION OF AN AUTOMATED COAGULATION ANALYZER

1987 ◽  
Author(s):  
M Johnston ◽  
M Andrew
Keyword(s):  
Thrombolytic Therapy ◽  
Light Source ◽  
Therapy Group ◽  
Screening Tests ◽  
Poor Correlation ◽  
Mean Values ◽  
Halogen Light ◽  
Halogen Light Source ◽  
Scientific Group ◽  
Time Required

The ACL (IL-Automated Coagulation Laboratory from the Fisher Scientific Group) is the first microcentrifugal analyzer incorporating 2 reading channels, a coagulometric channel consisting of a laser light source and a chromogenic channel consisting of a halogen light source. We have evaluated the instrument for precision and accuracy using different reagents for both clotting and the chromogenic assays. Replicate samples were run in both the PT and APTT modes using 4 different reagents. The reagent with the least particles had the greatest precision. The mean values for APTTs and PTs using a particle free reagent were 68.7 ± .83“ for the APTT (C.V. 1.2%), and 30.2 ± .33” (C.V. 1.1%) for the PT. A fibrinogen assay measured on the ACL (delta light scatter of the prothrombin time) was compared to the Clause fibrinogen assay in three population groups: the adult, the newborn and patients receiving thrombolytic therapy. The correlation for the adult and newborn was good with r values of .911 (n = 51) and .96 (n = 36) respectively. The thrombolytic therapy group had poor correlation r = .32. Antithrombin III (ATIII) and a2 antiplasmin (AP) assays were measured on the ACL using IIs chromogenic method. These were compared to an ATIII chromogenic method (Kahle) using a Gilford SBA 300 analyzer and α2 AP assay using a Protopath (Dade). The correlations were ATIII, r=.95 and α2 AP, r=.82. The plasminogen method of Friberger was adapted to the ACL giving us comparable results to those read off the Gilford SBA 300 (r=.93). With the introduction of the ACL we have been able to: 1) reduce the technical time required for assays by one half; 2) reduce reagent costs by one half to three-quarters; 3) reduce the amount of plasma required for screening tests by half the volume, which has greatly facilitated neonatal coagulation testing

P1595Increased in vivo perpetuation of whole-heart ventricular arrhythmia in heterozygous Na+/Ca2+-exchanger knockout mice

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
N Boegeholz ◽  
V Knappe ◽  
P Pauls ◽  
G Nickenig ◽  
L Eckardt ◽  
...  
Keyword(s):  
Single Cell ◽  
Mechanistic Explanation ◽  
Cellular Level ◽  
Qtc Interval ◽  
Burst Stimulation ◽  
Innovative Strategies ◽  
Whole Heart ◽  
The Right

Abstract Background Commonly, innovative antiarrhythmic strategies are derived from single cell studies that frequently yield promising in vitro findings. However, these results may differ on the whole-heart level, since multicellular electrophysiology is characterized by several emergent features. In previous cellular studies, we have identified the Na+/Ca2+-exchanger (NCX) as a promising target for an innovative antiarrhythmic strategy, as NCX upregulation is present in major cardiac diseases (e.g. heart failure) and promotes independently cellular early and late afterdepolarizations (EADs and DADs). Vice versa, we found that genetic and pharmacological NCX inhibition protects against EADs and DADs. To date, it is unknown, whether the concept of NCX inhibition indeed beneficially applies to the whole-heart level. Thus, we here investigate the in vivo inducibility and perpetuation of whole-heart arrhythmia using a heterozygous NCX-knockout mouse (KO) model that is protected against EADs and DADs on the cellular level. Methods/Results Programmed electrical right ventricular stimulation (PVS) and burst stimulation were performed in KO (n=22) and wild-type (n=34) mice by an octapolar mouse electrophysiological catheter introduced via the right jugular vein. Inducibility for ventricular tachycardia (VT) during PVS was similar in WT (73.5%) compared to KO (90.0%) (p=0.1707). With burst stimulation, VT inducibility was higher in KO (KO: 68.2%; WT: 32.4%; p=0.0134). During PVS, KO exhibited increased VT perpetuation as reflected in a significantly prolonged mean (in s; KO: 0.89±0.93; WT: 0.39±0.41; p=0.0097) and cumulative VT duration (in s; KO: 19.54±27.98; WT: 4.46±6.35; p=0.0019). Analysis of animals that were inducible for VT consistently yielded similar results. The ventricular refractory period (VRP) (in ms; KO: 15.1±3.5; WT: 18.7±4.1; p=0.0050) and the QTc interval were shortened in KO (in ms; KO: 46.5±5.8; WT: 53.2±5.9; p=0.0001). Conclusions As opposed to findings on the single cell level, KO mice exhibited an increased in vivo arrhythmia burden on the whole-heart level during PVS. This mainly resulted from increased perpetuation of artificially induced VTs, since the inducibility of VTs was not significantly increased in KO with PVS. As a mechanistic explanation of these surprising results, we found significantly reduced VRP and QTc durations in KO in line with the previously demonstrated action potential shortening in single KO cardiomyocytes, which promotes the perpetuation of VTs. We conclude that genetic NCX inhibition can protect from proarrhythmic cellular triggers like EADs and DADs that can initiate VT. However, VTs may perpetuate longer in KO most likely due to reduced refractory periods. This finding carries important translational limitations for the antiarrhythmic concept of NCX inhibition and demonstrates that the value of novel innovative strategies needs evaluation on both the cellular and the whole-heart level. Acknowledgement/Funding None

Sign in / Sign up

Export Citation Format

Share Document