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Microscopy and Imaging

Making the Perfect Blood Smear

Stop wasting time throwing out slide after slide trying to create a readable blood smear. Read our how-to guide for creating the perfect blood smear slide.

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What Can Electron Microscopy Do for You?

The electron microscope (EM) – where electrons, rather than photons, make the image – fell out of fashion for a while, but it has come back refreshed. Modern electron microscopes cost less, use less electricity, and are generally easier to maintain than the older models, so it is likely that you can get your hands on one. Read on to learn more about this technique, and how to implement it into your research.

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Microscope Disinfection: A Quick Guide

Shared microscopes have the potential to get dirty and spread nasties between samples and users. Check out our quick guide on how to clean and disinfect your microscope.

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Ultramicrotomy for Electron Microscopy

Ultramicrotomy is the process by which a sample is cut into very thin slices or “sections”, usually for imaging by transmission electron microscopy (TEM) or relatively new techniques using scanning electron microscopy (See Array tomography in three dimensional scanning electron microscopy for biology). This technique requires a bit of finesse, and this article will help…

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Microscope Finder Slides: Their History, Development, and Use

Have you ever been looking through a box of slides and found something that you want to image or look at later, or even show to one of your colleagues or supervisor? Finding that exact spot on the slide at a later date can prove to be difficult- using a marker pen on the coverslip…

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Laser in a droplet

When you hear about a laser, you likely imagine a medium-size apparatus with a light beam coming out of it, not a bacterium in a drop of liquid. Well, Turkish and British scientists went beyond ordinary imagination – they expressed a fluorescent protein in E.coli and suspended live bacteria in droplets. Illuminated droplets served as…

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An Introduction to Cardiac Optical Mapping

What Is Optical Mapping and How Is It Used? Synchronisation of the contraction of heart muscle is essential for the efficient pumping of blood through the circulatory system. Cardiac contraction is controlled by the regulated spread of electrical impulses from cell-to-cell within the heart.  In pathological conditions, these electrical impulses can become disordered and lead…

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Automated Image Analysis – the Future of Data Acquisition?

Automated image analysis uses finely tuned software to extract data from digital images. Algorithms recognize specific shapes and patterns in the images and gather quantitative information that is then used for further data analysis. The pharmaceutical and biological research industries have benefitted greatly from this technology, which allows researchers to analyze hundreds—if not thousands—of samples…

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Safranin: Cheap Stain to Visualize Chromosomes

As an undergraduate student, one of the first experiments I did was staining chromosomes in mitotically active onion root tip cells. The stains that are conventionally used for this purpose are acetocarmine or aceto-orcein (which smell like vinegar). However, the cost of these stains is quite high. Personally, I find safranin, which is another stain, more…

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Get Your Microscopy Mojo Back with Our Image Acquisition and Processing Tips

Ever since the invention of the first compound microscope by Zacharias Jansen in 1590, our understanding of the microscopic world has grown exponentially. Microscopes have evolved from mere assemblies of magnifying lenses to extremely powerful tools for visualization on the atomic scale. You can find a wealth of information on the workings of a microscope…

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Color Transmission Electron Microscopy

There are two types of electron microscopy—transmission electron microscopy (TEM) and scanning electron microscopy (SEM). SEM creates fascinating 2D images by bouncing electrons off the surface of the sample. I highly recommend searching for SEM samples on Google images. There are a wide variety of applications for electron microscopy. While SEM images are aesthetically amazing,…

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From Cells to Scope: Chamber Slide Immunochemistry

Immunolabeling is the tried-and-true immunochemistry method of getting the stain you want onto the molecular target you want. Whether that target is contained within a large region of tissue (immunohistochemistry) or inside a single cell (immunocytochemistry), the ability to accurately label large numbers of samples will simplify your workflow and help you to achieve excellent…

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Lasers for Confocal Microscopy: Part II

Continuing from our first article on lasers for confocal microscopy, we will now discuss two specialized types of lasers: lasers for two-photon excitation and tunable, white light lasers. We will also discuss the applications of the two lasers. Lasers for Two-Photon Excitation The two-photon absorption phenomenon was first described for microscopy in 1931. Here, the…

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Things to Consider When Buying a Microscope Camera (Part 2)

In the first part of this series, we discussed the differences between a color and a monochrome microscope camera and when one is advantageous over the other. We also touched on the subject of optimal camera resolution for a given imaging system. In this part, we will tackle a few additional camera specifications and how…

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Things to Consider When Buying a Microscope Camera (Part 1)

Purchasing a microscope camera is one of the most daunting tasks you might have to undertake. Before you set out to buy that camera, carefully consider your applications. Things like sample brightness or the speed of the phenomenon you are trying to capture can dictate your choices. Also, this is the time to make peace…

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All You Need to Know (and More) About Embedding for Electron Microscopy

Interested in the detailed structure of your tissue? High-resolution imaging techniques, such as brain electron microscopy, provide an intricate view of your tissue. While it may be a rather complicated procedure with nasty chemicals, the advantages of epon embedding can make it the best choice for morphological studies. The hard blocks are excellent for structural…

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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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Unpacking the Daunting Task of Stereology for Electron Microscopy

Unpacking the Daunting Task of Stereology for Electron Microscopy Electron microscopy provides fantastic detail and resolution, with brain electron microscopy allowing visualisation of neurons and their individual synaptic connections. You may find yourself needing to count these neurons or connections, which can easily go into the billions. But counting these one-by-one isn’t really feasible. This…

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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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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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Tips for Peering into the Interior of Mice Using Intravital Microscopy

Techniques to study entire tissues, such as brain imaging microscopy, provide great insight into the biology of the whole tissue, rather than just individual cells.  Taking this one step further is intravital microscopy (IVM); a newer approach for the imaging of living tissues and organs in live animals. A wide variety of organs can be…

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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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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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The Art and Science of Figure Creation: Think BIG to see Small

There are those of us who began our careers literally in the dark. Yes, there was a time and not that long ago, that all figures had to be on film. Slide presentations were slides. Micrographs were, well, micrographs on film. Figure creation involved several steps: figures for publications had to be mocked up; then…

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Halogen vs LED Lighting in Digital Microscopy

When it comes to light sources for microscopy, there is really no such thing as the “best.” The type of light source you use depends on the system you are working with and the type of result that you want. Digital systems are usually designed to work with either a halogen or a LED light…

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Challenges of Autofluorescence in Neuroscience

If you have ever imaged biological samples, you have likely encountered autofluorescence. That pesky background coloration you see under the microscope, which can make it difficult to distinguish your actual signal from the noise.1 When you are trying to look for something as delicate as RNA, you don’t want to be hunting for your signal…

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How to Maintain Live Cells on a Microscope Stage

Are you preparing to set up live cell imaging experiments? You’ve got all your cell lines, antibodies, reagents, and protocol ready. You just want to wake up in the morning and enter into that dark room. Well, think again!! As we (I mean the cell biologists) always say, happy cells mean happy life. You have…

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