Machine Learning for Analysis of Microscopy Images: A Practical Guide and Latest Trends.

The explosive growth of Machine Learning provided scientists with insights into the data in the ways unattainable using established research techniques. It allowed the detection of biological features that were previously unrecognized and overlooked. Yet, since Machine Learning methodology originates from informatics, many cell biology laboratories experience difficulties with implementing it.

Machine Learning for Analysis of Microscopy Images: A Practical Guide.

The explosive growth of machine learning has provided scientists with insights into data in ways unattainable using prior research techniques. It has allowed the detection of biological features that were previously unrecognized and overlooked. However, because machine-learning methodology originates from informatics, many cell biology labs have experienced difficulties in implementing this approach.

Mobile Quantitative Colocalization Analysis of Fluorescence Microscopy Images.

Understanding the nature of fluorescently-labelled molecules requires proper quantification of their colocalization. We developed a new approach to enable quantification of colocalization of markers in fluorescence microscopy images using mobile computers. It consists of three interacting components: desktop computer - cloud - mobile device.

Quantitative colocalization analysis of fluorescence microscopy images.

Colocalization is an important finding in many cell biological studies. This unit describes a protocol for quantitative evaluation of fluorescence microscopy images with colocalization based on calculation of a number of specialized coefficients. Images of double-stained sections are first subjected to background correction, and then various coefficients are calculated.

Bridging the gap between qualitative and quantitative colocalization results in fluorescence microscopy studies.

Quantitative colocalization studies suffer from the lack of unified approach to interpret obtained results. We developed a tool to characterize the results of colocalization experiments in a way so that they are understandable and comparable both qualitatively and quantitatively. Employing a fuzzy system model and computer simulation, we produced a set of just five linguistic variables tied to the values of popular colocalization coefficients: "Very Weak", "Weak", "Moderate", "Strong", and "Very Strong".

Critical evaluation of quantitative colocalization analysis in confocal fluorescence microscopy.

Spatial colocalization of fluorescently labeled proteins can reveal valuable information about proteinprotein interactions. Compared to qualitative visual interpretation of dual color images, quantitative colocalization analysis (QCA) provides more objective evaluations to the degree of colocalization. However, the finite resolution power of microscopes and the spatial patterns of intracellular structures may compromise the reliability of many classical QCA methods.

Quantifying spatial correlations of fluorescent markers using enhanced background reduction with protein proximity index and correlation coefficient estimations.

Interactions of proteins are examined by detecting their overlap using fluorescent markers. The observed overlap is then quantified to serve as a measure of spatial correlation. A major drawback of this approach is that it can produce false values because of the properties of the image background.

Quantitative colocalization analysis of confocal fluorescence microscopy images.

Colocalization is an important finding in many cell biological studies. This unit describes a protocol for quantitative evaluation of images with colocalization based on the calculation of a number of specialized coefficients. First, images of double-stained sections are subjected to background correction.

Recent advances in quantitative colocalization analysis: focus on neuroscience.

Quantitative colocalization analysis is an advanced digital imaging tool to characterize the spatial expression of molecules of interest in immunofluorescence images obtained using confocal microscopes. It began from simple pixel counting and, with introduction of specialized algorithms, transformed into a powerful image analyzing technique capable of identifying the exact locations of various molecules in tissues and cells and describing their subtle changes in dynamics. Applications of quantitative colocalization in the field of neuroscience proved to be particularly informative by helping to obtain observations not otherwise achievable using other techniques.

TLS-GFP cannot rescue mRNP formation near spines and spine phenotype in TLS-KO.

RNA-binding protein TLS transports Nd1-L mRNA, which encodes an actin-stabilizing protein, to the neuronal dendrites. TLS-null mouse (TLS-KO) hippocampal neurons display abnormal spine morphology, and thus could be attributed to actin destabilization by the improper supply of Nd1-L mRNA to the dendrites. In this study, we showed that the exogenous expression of TLS in TLS-KO neurons did not rescue the abnormal spine phenotypes.

Quantitative colocalization analysis of confocal fluorescence microscopy images.

Colocalization is an important finding in many cell biological studies. This unit describes a protocol for quantitative evaluation of images with colocalization based on the calculation of a number of specialized coefficients. First, images of double-stained sections are subjected to background correction.

Quantitative colocalization analysis of multicolor confocal immunofluorescence microscopy images: pushing pixels to explore biological phenomena.

Quantitative colocalization analysis is an advanced digital imaging tool to examine antigens of interest in immunofluorescence images obtained using confocal microscopes. It employs specialized algorithms to estimate the degree of overlap of fluorescence signals and thus enables acquiring important new information not otherwise obtainable using qualitative approaches alone. As raw confocal images have high levels of background, they should be prepared to become suitable for reliable calculation of colocalization coefficients by correcting it.

Ethanol consumption alters expression and colocalization of bile salt export pump and multidrug resistance protein 2 in the rat.

Chronic ethanol consumption elicits detrimental changes of liver metabolism. By employing a 12-week-long feeding regimen, we investigated the effects of chronic ethanol consumption on the expression and localization of bile salt export pump (Bsep), a major canalicular exporter of bile salts, and multidrug resistance protein 2 (Mrp2), a canalicular organic anion transporter, in the rat liver. RT-PCR, confocal immunofluorescence microscopy, immunoblotting, and quantitative colocalization analysis were used to examine their gene and protein expression, and changes in the distribution of antigenic sites.

Experimental LPS-induced cholestasis alters subcellular distribution and affects colocalization of Mrp2 and Bsep proteins: a quantitative colocalization study.

Quantitative colocalization analysis is a powerful tool for reliable estimation of the colocalization of antigens. We employed it to determine the changes of colocalization of multidrug resistance protein 2 (Mrp2) and bile salt export pump (Bsep) in confocal immunofluorescence microscopy images of rat liver following lipopolysaccharide (LPS) administration. Samples were taken 2, 24, 48 hours, and 1 week after LPS challenge.

Direct action of platelet activating factor (PAF) induces eosinophil accumulation and enhances expression of PAF receptors in conjunctivitis.

Purpose: The goal of the present study was to investigate the role of platelet activating factor (PAF) and PAF receptor (PAF-R) in the recruitment of eosinophils into the conjunctiva in the course of PAF induced conjunctivitis. Eosinophils are important players in the immediate hypersensitivity reactions and in allergic conjunctivitis. PAF-R is expressed in many ocular tissues including conjunctival cells.

Localization of the PE methylation pathway and SR-BI to the canalicular membrane: evidence for apical PC biosynthesis that may promote biliary excretion of phospholipid and cholesterol.

To better understand the regulation of biliary phospholipid and cholesterol excretion, canalicular membranes were isolated from the livers of C57BL/6J mice and abundant proteins separated by SDS-PAGE and identified by matrix-assisted laser desorption/ionization mass spectrometry. A prominent protein revealed by this analysis was betaine homocysteine methyltransferase (BHMT). This enzyme catalyzes the first step in a three-enzyme pathway that promotes the methylation of phosphatidylethanolamine (PE) to phosphatidylcholine (PC).

Analgesic effects of ketamine ointment in patients with complex regional pain syndrome type 1.

Objective: Ketamine hydrochloride (KET), an agent used for general anesthesia, has local anesthetic effects and N-methyl-D-aspartate (NMDA) receptor antagonist action. Because recent studies emphasized the role of peripherally distributed NMDA receptors in processing the nociceptive information, we investigated whether peripheral application of the ointment containing KET is able to attenuate the symptoms of local neuropathic pain.

Case Reports: We applied ointment containing KET (0.

Combined biochemistry and histocytochemistry as a tool to investigate Ecto-ATPase in the cardiac muscle.

Ecto-ATPase (ecto-adenosine triphosphatase), a key enzyme of cardiac metabolism, is responsible for modulation of the concentration of extracellular nucleotides in the heart. We present methodology consisting of the combined use of biochemical and histocytochemical techniques to study its properties. Using samples from essentially the same preparation, we applied biochemistry and histocytochemistry to determine biochemical characteristics of ecto-ATPase and an in situ localization of its reactivity.

Lipopolysaccharide administration increases acid and alkaline phosphatase reactivity in the cardiac muscle.

The effect of lipopolysaccharide (LPS) administration on the in situ distribution of the reaction product of acid phosphatase (AcPase) and alkaline phosphatase (AlPase) activity was examined in the rat cardiac muscle using catalytical cytochemistry. Tissues of the heart were fixed and then incubated in reaction media for detection of AcPase and AlPase reactivity. In normal hearts, reaction product of AcPase activity was observed in lysosomes.

Asynchronous expression and colocalization of Bsep and Mrp2 during development of rat liver.

In the liver, function of the bile salt export pump (Bsep), a major canalicular exporter of bile salts, is complemented by activity of the multidrug resistance protein 2 (Mrp2), a canalicular organic anions transporter. Mrp2 was found capable of transporting various anticancer drugs out of cells, eventually undermining their therapeutic potential and contributing to multidrug resistance. We employed a RT-PCR, immunoblotting, and immunofluorescence to examine their gene, protein expression, and distribution of antigenic sites in the rat liver during development from 16-day-old fetus to adult animal.