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Direct, two-dimensional counting or measuring of cells as they appear in histological sections is subject to a number of artifacts that can lead to erroneous conclusions about changes in cellular populations. Numerous correction procedures devised to compensate for these artifacts are collectively termed model-based stereology due to their reliance on a model of cell geometry for correction formulas...
Real-time three-dimensional (RT3D) ultrasound is a relatively new imaging modality that uses a special ultrasound transducer consisting of a matrix array of elements. The array electronically steers an ultrasound beam to interrogate a 3D volume of tissue. The real-time nature of RT3D ultrasound differentiates it from reconstructed 3D ultrasound, in which a conventional ultrasound transducer is moved...
The mouse has become the de facto model for the majority of atherosclerosis studies. Studies involving the quantification of lesions in mouse models of the disease represent the basis of our evolving concepts on the biochemical and cellular mechanisms underlying the atherogenic process. Many issues of experimental design, including specific model, strain, gender, atherogenic stimulus, duration of...
Mitochondria are crucial for many aspects of cellular homeostasis and a sufficiently negative membrane potential (Δψ) across the mitochondrial inner membrane (MIM) is required to sustain most mitochondrial functions including ATP generation, MIM fusion, and calcium uptake and release. Here, we present a microscopy approach for automated quantification of Δψ and mitochondrial position, shape and calcium...
In vitro three-dimensional models of cancer have the ability to recapitulate many features of tumors found in vivo, including cell–cell and cell–matrix interactions, microenvironments that become hypoxic and acidic, and other barriers to effective therapy. These model tumors can be large, highly complex, heterogeneous, and undergo time-dependent growth and treatment response processes that are difficult...
Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of Drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in Drosophila spans all scales from single molecules to the entire populations of adult organisms, from...
The majority of reports in which microvascular network properties are quantified rely on manual measurements, which are time consuming to collect and somewhat subjective. Despite some progress in creating automated image analysis techniques, the parameters measured by these methods are limited. For example, no automated system has yet been able to measure support cell recruitment, which is an important...
Fluorescence and bioluminescence time-lapse imaging allows to investigate a vast range of cellular processes at single-cell or even subcellular resolution. In particular, time-lapse imaging can provide uniquely detailed information on the fine kinetics of transcription, as well as on biological oscillations such as the circadian and cell cycles. However, we face a paucity of automated methods to quantify...
•STED (stimulated emission depletion) is a popular super-resolution fluorescence microscopy technique. •In this paper, we present a concise guide to building a resonant-scanning STED microscope with ultrafast photon-counting acquisition. •The STED microscope has two channels, using a pulsed laser and a continuous-wave (CW) laser as the depletion laser source, respectively. •The CW STED channel...
Biologists increasingly use co-culture systems in which two or more cell types are grown in cell culture together in order to better model cells’ native microenvironments. Co-cultures are often required for cell survival or proliferation, or to maintain physiological functioning in vitro. Having two cell types co-exist in culture, however, poses several challenges, including difficulties distinguishing...
Advances in fluorescent probe design and synthesis have allowed the uniform in situ labeling of individual RNA molecules. In a technique referred to as single molecule RNA FISH (smRNA FISH), the labeled RNA molecules can be imaged as diffraction-limited spots and counted using image analysis algorithms. Single RNA counting has provided valuable insights into the process of gene regulation. This microscopy-based...
In order to study the detailed assembly and regulation mechanisms of complex structures and machineries in the cell, simultaneous in situ observation of all the individual interacting components should be achieved. Multi-color Single-Molecule Localization Microscopy (SMLM) is ideally suited for these quantifications. Here, we build on previous developments and thoroughly discuss a protocol for two-color...
The microscopic analysis of telomere features provides a wealth of information on the mechanism by which tumor cells maintain their unlimited proliferative potential. Accordingly, the analysis of telomeres in tissue sections of patient tumor samples can be exploited to obtain diagnostic information and to define tumor subgroups. In many instances, however, analysis of the image data is conducted by...
Podosomes are adhesive structures formed on the plasma membrane abutting the extracellular matrix of macrophages, osteoclasts, and dendritic cells. They consist of an f-actin core and a ring structure composed of integrins and integrin-associated proteins. The podosome ring plays a major role in adhesion to the underlying extracellular matrix, but its detailed structure is poorly understood. Recently,...
We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel...
This review aims at providing a practical overview of the use of statistical features and associated data science methods in bioimage informatics. To achieve a quantitative link between images and biological concepts, one typically replaces an object coming from an image (a segmented cell or intracellular object, a pattern of expression or localisation, even a whole image) by a vector of numbers....
Organotypic in vitro culture of 3D spheroids in an extracellular matrix represent a promising cancer therapy prediction model for personalized medicine screens due to their controlled experimental conditions and physiological similarities to in vivo conditions. As in tumors in vivo, 3D invasion cultures identify intratumor heterogeneity of growth, invasion and apoptosis induction by cytotoxic therapy...
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