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Microscopy & Imaging

The A to Z of Histological Stains

With the use of stains and dyes, histology allows researchers to visualize particular tissue structures, chemical elements within cells, tissues and even microorganisms. The advent and evolution of histology follows that of microscopy as outlined in ‘A (very) Short History of Histology’. Histology, which means ‘tissue science’ became an academic discipline in its own right…

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Tissue Embedding Throwdown: Paraffin vs OCT vs Resin

Tissue embedding and sectioning is a backbone of many biological research labs. While commiserating with other grad students over tedious hours spent in the lab, you’re probably aware that there is more than one way to slice up a chunk of tissue. We’ve previously introduced what to consider when choosing a tissue embedding medium and…

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How to Use CellProfiler for Cell Imaging

Are you trying to figure out how to calculate intensities of fluorescently-labeled single cells? Do you have cells at high densities or present in clusters? Are you worried that your current cell imaging analysis software is unable to mark clear boundaries around each cell in a cell cluster? Don’t fear, because CellProfiler 2.1 is here to…

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How to Obtain Stellar Staining with Fluorescent IHC

They say “a picture is worth a thousand words.” This is especially true in the case of fluorescent immunohistochemistry (IHC). With the flip of a microscope filter, you can gaze into a brightly colored galaxy of red, green, and blue pixels, waiting to be captured and presented in your next publication. If you are interested in…

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Detecting Cell Apoptosis on Tissue Slides

Apoptosis, or programmed cell death, is a physiological process in which individual cells are set to die without harming their environment. It involves a cascade of complex and tightly regulated cellular events. Detecting apoptosis on tissue slides, involves either detecting the molecular participants of these events, or the morphological changes that occur on the cellular…

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Automated Microscopy

The traditional microscope that you know and love is operated manually. Picture the scene: the microscopist chooses the light source, gently places the sample the moveable stage, selects the objective lens, and scans to select the field of view. This process is perfect for processing and analyzing a small number of samples per day. But…

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Sample Preparation for Scanning Electron Microscopy

Proper sample preparation plays an important role in obtaining the required information when using scanning electron microscopy (SEM). You need to consider the sample’s size, shape, state, and conductive properties prior to sample preparation. Ideally, the smallest representative sample size is the one to use. The microscope’s detection capacity is as much as 1µm from…

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In Situ Zymography: Let’s Catch that Enzyme in Action!

In situ zymography (ISZ) is the best choice to study proteases. Proteases are a challenge to study as proteases are extremely potent enzymes. As such, they need to be controlled at multiple levels to prevent them from being unleashed and making a cellular mess. Regulation of their activity occurs at virtually all levels: transcriptional control,…

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Automated Cell Counting with a Fluorescent Twist

Cell counting is the bane of existence of many researchers. Countless hours spent in front of the microscope with a haemocytometer on the stand and a manual tally (or “clicker”) in hand can be really daunting. Not to mention that no one will ever double check your count if you don’t take a picture. Those…

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Analyze Immunostained Slides with Semiquantitative Scoring

A  routine task in the lab is to investigate the presence of your favorite protein in a range of histological samples. No doubt, staining your tissue sections using good old immunohistochemistry (IHC) would be your first choice. You just got to love a technique that has celebrated its 70th birthday, and is still used in…

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Data Analysis for Three-dimensional Volume Scanning Electron Microscopy

In recent years, three-dimensional (3D) scanning electron microscopy techniques have gained recognition in the biological sciences. In particular, array tomography, serial block face scanning electron microscopy (SBFSEM) and focused ion beam scanning electron microscopy (FIBSEM) (described in Three-Dimensional Scanning Electron Microscopy for Biology) have shown an increase in biological applications, elucidating ultrastructural details of cells…

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Can You Stand the Cold? Cryosectioning for Beginners

Before you can perform histology on your tissue samples – you need to prep them. This means you must fix them, embed them and section them into thin slices for analysis. A great way to slice your tissues is cryosectioning. But cryosectioning is not so great when it your tissues melt, fold, curl, wrinkle, tear,…

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Microscopy – a Numbers Game

While the microscope is synonymous with biology, it is a child of physics and technology. When we learn about the microscope we learn physics—specifically, we learn about optics. Many great resources are available that explain the inner working of microscopy. And, like most things in physics, the inner working of microscopes comes down to a numbers…

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