bluuebunny/crossref_metadata_2025 huggingface dataset:
Image Stitching Using Photoshop
Authors: Sedgewick Jerry
Published: March 2018

Several images can be stitched together (sometimes referred to as “montaging”) through the use of Photoshop. Edges of the images can be feathered and the process automated to reduce the hours of work that can go into this procedure.

Before going any further, let me be quick to say that more than one company has developed protocols to accomplish image stitching. When your lab is looking at large fields, while needing to resolve fine details, then I would strongly recommend the purchase of a system designed for this purpose. Issues surrounding motorized stage accuracy, problems with tilting when a camera is perched on a long optical tube, and image to image correction for contrast, color and uneven illumination can all contribute to confounding issues when image stitching. These companies have worked through these problems with off-the-shelf systems.
Confocal Microscopy System Performance: Axial Resolution
Authors: Zucker Robert M
Published: March 2018

The confocal laser-scanning microscope (CLSM) has enormous potential in many biological fields. When tests are made to evaluate the performance of a CLSM, the usual subjective assessment is accomplished by using a histological test slide to create a “pretty picture.” Without the use of functional tests many of the machines may be working at sub-optimal performance levels, delivering sub optimum performance, and possibly misleading data. In order to replace the subjectivity in evaluating a confocal microscope, tests were derived or perfected that measure field illumination, lens clarity, laser power, laser stability, dkhroic functionality, spectral registration, axial resolution, scanning stability, PMT quality, overall machine stability, and system noise (1-3). It is anticipated by using this type of test data, performance standards for confocal microscopes will be obtained and the current subjectivity in evaluating CLSM performance will be eliminated.
Microwave Mechanisms — The Energy/Heat Dichoto
Authors: Galvez Jose J , Giberson Richard T , Cardiff Robert D
Published: March 2018

The current use of microwave technology in science creates a dichotomy. Is it the heat or is it the energy? One entire branch of science, chemistry, uses microwave energy to apply heat to a broad range of chemical processes, under pressure, to produce the desired end-products quickly and efficiently (1). The biological sciences, surgical pathology in particular, have tried to adapt the microwave oven to speed up a broad range of processes: fixation, decalcification, antigen retrieval, tissue processing for paraffin and plastic embedding, and histological staining, including special stains, immunolabeling, and in situ hybridization (2). The biologists have assumed that they are also applying heat to speed processing. However, recent improvements in the microwave suggest that the energy is the critical variable (9). We have designed fixation experiments to test the two views.
Guidance for Choosing When to Use Electron and/or Light Microscopy and Related ASTM E4 Standards
Authors: Nester R C
Published: March 2018

Technical publications sometimes include scanning electron images to characterize a microstructure, when the relevant structure could have very easily been illustrated using a simple light micrograph. When should one use a light generated image? What are the advantages/disadvantages of an electron generated image, particularly; one generated using a scanning electron microscope (SEM)? While there is some overlap in the capabilities of these imaging systems; in general, they are complementary tools, each with their own uses. Standards under the jurisdiction of ASTM Committee E4 on Metallography offer guidance to both new and experienced users of both investigative techniques.
TEM Specimen Preparation Technique For Small Semiconductor Devices
Authors: Hudson Mark , Benedict John , Flaitz Philip
Published: March 2018

One of the methods of preparing samples for analysis by Transmission Electron Microscopy (TEM) is the well-known procedure using a Tripod polisher and the wedge technique (1-3), developed in our laboratory. Though developed explicitly for preparing samples of integrated circuit structures built on silicon, the technique has been used in our lab for a wide variety of other materials, including metals and ceramics. In general when working with silicon samples, we have the luxury of starting with large wafer pieces or chips that are generally at least a couple of millimeters square or larger. Recently, however, we needed to work for an extended period on GaAs based lasers, where the devices requiring analysis were individual lasers extracted from individual packages. These small samples, measuring 100x100x50 microns, are too small for the manual handling involved in routine mechanical cross sectioning methods.
Scanning Wet Specimens
Authors: Carmichael Stephen W
Published: March 2018

Would it be useful if you could examine a wet, perhaps even a living, specimen in the scanning electron microscope? Of course we think that this would be impossible, given the vacuum the specimen would be subjected to in the microscope. However, in the realm of materials research, the Environmental Scanning Electron Microscope (ESEM) is being developed. Apparently this instrument has not been fully appreciated and utilized by biologists.

As reviewed by Athene Donald, a pioneer in developing the ESEM, this instrument has been commercially available for a decade. It is still evolving as a useful tool in looking at materials such as cement, natural fibers, and aqueous dispersions. Applications of the ESEM. to biological Studies are extremely limited. However, studies on biological samples, even living cells, are possible (although not without problems and limitations).
New CMEIAS Image Analysis Software for Computer-Assisted Microscopy of Microorganisms and Their Ecology
Authors: Dazzo Frank B
Published: March 2018

Microscopy is one of the most important techniques in microbial ecology, since this is the most direct approach to examine the microbe's world from its own perspective and spatial scale. The value of quantitative microscopy in studies of microbial ecology can be increased even further when used in conjunction with computer assisted image analysis. There are two main advantages of using digital image processing and pattern recognition techniques in conjunction with microscopy for quantitative studies of microbial ecology. First, automatic image analysis reduces the amount of tedious work with microscopes needed to accurately quantify in situ morphological diversity, abundance and metabolic activity of microbes. Secondly, these techniques provide an important quantitative tool that can significantly enhance the polyphasic analysis of the structure, diversity, spatial features, and functions of complex microbial communities in situ without cultivation.
Making Slide Shows in Acrobat
Authors: Sedgewick Jerry
Published: March 2018

PowerPoint has traditionally been the software of choice for slide shows tit conferences and meetings. Its ease of use has made the program ideal, along with its universality among scientists and engineers.

The program does have its drawbacks, however. Most notably, it is saved in a format that essentially makes it unusable for any other purpose than that of a slide show. It cannot be used for publication, and, as many discover all too late, it is not the software of choice for making posters (both these phenomena go back to Microsoft's refusal to pay a license to Adobe for PostScript, the universally used “page description language” among publishers). The remainder of the drawbacks exist when the slide show needs to be distributed. Newer versions of PowerPoint can make HTML files for posting on a web site by using Save As under File, but saving in the PowerPoint format has not evolved as a way to view slide shows on the web.
Basic Stereology
Authors: Basgen John M
Published: March 2018

Many us who use microscopes are interested in the internal structure or components of three-dimensional objects. Often we must section these objects to observe these internal components. For many years, microtomes have been used to make physical sections, but in recent years confocal microscopes, MR imaging, CT scanners, and even standard optical microscopes have been used to obtain “optical” sections. Two-dimensional images of these different types of sections can be used to extract three-dimensional quantitative information about the objects and their internal components, The sectioning process reduces the observed dimensions of the object and components. With apologies to Rene Magritte, the structure portrayed in Figure 1 is not a three-dimensional glomerulus but a two-dimensional profile of a glomerulus. In most cases, interest is on the structure of the three-dimensional object and not the structure in the two-dimensional image. Thus, care must be taken when obtaining and interpreting data from two-dimensional images.
Rediscovery of Darkfieid Dispersion Staining while Building a Universal Student Microscope
Authors: Clarke Theodore M
Published: March 2018

My first universal student microscope, shown in Figure 1, began life as a Monolux microscope from the 1960rs. Its development into a universal student microscope began when my wife wanted a polarized light microscope with the ability to photograph microscopic crystals under a cover glass for their artistic value. My background as a metallurgist was with the reflected light metallurgical microscope, I have also designed and built vertical illuminators for brightfield illumination of complete metal log raphic specimens using a fiber optic light guide end as the light source with lens configurations giving an imaged field diaphragm and an illumination aperture diaphragm imaged in the aperture of the macro lens.
Creating Multimedia Teaching and Training Tools
Authors: Barlow Steven B
Published: March 2018

Teaching and training users how to operate laboratory equipment is a time-intensive practice. Many new users are students, who have generally high turnover rates; after they complete a class project or degree program, they leave the facility, In addition, users often divide their time among a variety of techniques and equipment. With episodic usage, researchers tend to forget details of instrument operation and need to be retrained. Academic core facilities must balance their productivity against the time it takes to train and retrain an ever-changing parade of users. Site-specific multimedia teaching and training resources, such as films, CDs, videos, or DVDs, if easily available in the laboratory, would enable users to refresh and retrain themselves on equipment operation.
Tardigrades and Microscopes
Authors: Miller William R
Published: March 2018

Commonly known as 'water bears', tardigrades are a phylum of microscopic animals that can be found living on mosses and lichens all over the world. The name Tardigrada means 'slow walker' which describes their sluggish, deliberate movements. Between these slow movements and their 'teddy bear' like appearance, tardigrades are the only really “cute” invertebrate. Tardigrades, Echiniscus sp., are generally less than 500 micrometers in length and require at least40-power magnification to be seen clearly.
Cryoelectron Tomography
Authors: Carmichael Stephen W
Published: March 2018

We have all seen beautiful three-dimensional (3D) renderings of molecular models, complete with helices and pleated sheets. And for more than half a century we have also seen electron micrographs of cellular structures, although usually in two dimensions. There has been a gap between these two sets of images. By developing a technique that promises 3D images at resolutions approaching the molecular level, Ohad Medalia, Igor Weber, Achilleas Frangakis, Daniela Nicastro Günther Gerisch, and Wolfgang Baumeister have bridged that gap.
FTIR Hyperspectral Images of Microscopic Droplets of Splattered Blood
Authors: Huffman Scott W , Lukasiewicz Kara B , Brown Chris W
Published: March 2018

During forensic Investigations, determining the time frame of a crime can be an extremely important clue for solving the case. The exact time at which a crime was committed can be especially difficult to determine when considerable time has elapsed. To improve the predictive capabilities of crime scene investigators, we have focused on using spectroscopic methods to Investigate the aging of bloodstains.
Quality in Electron Microscopy
Authors: Bruton Tony , Chapman Steve , Harding Paul
Published: March 2018

Does quality exist in the electron microscope laboratory? What is quality? Quality is when a product or service meets all of the customers' requirements, is delivered in the correct quantity at the required time, to the right place and at a price the customer is prepared to pay.

In an open competitive environment all of the above would apply. In an electron microscope laboratory are we totally satisfied that we have given consideration to our product? We also provide a service, are we happy that the service we provide is of a sufficiently high standard, a standard that we would expect if we were the customers in a hotel or a garage? If we follow the example of world trends in industry, then simple product and service quality, in isolation, fs no longer sufficient, and focus must be given to a total quality approach.
Vehicle Fraud Detection Using Microscopy
Authors: Kruger Joshua J
Published: March 2018

In a criminal case, such as vehicle theft or vehicle hijacking, where a vehicle has been dismantled, the forensic scientist is many times faced with the problem of establishing the history of a specific auto body part. The normal method for doing this is by performing paint analysis. There are, however, a few shortcomings to paint analysis. In this paper another technique for determining the history of a body part is discussed, namely the comparison of surface replicas.
Preparing Drosophila for Tissue Processing
Authors: McManus Connie
Published: March 2018

All insects have an exoskeleton made of chitin, which is a protein that is hard and impervious to moisture. To enable processing reagents to more effectively enter the body cavity, a small slit in the abdomen can be made. For very small insects, such as the fruit fly, Drosophila, micro dissecting tools can be made from commonly found items such as insulated electrical wire, double edged razor blades and wood applicator sticks.
Brightfield Illumination of Large Field Sizes
Authors: Clarke Theodore M
Published: March 2018

Microscopists and scientific photographers sometimes find it desirable or necessary to record a larger field size than the lowest power objective can cover using brightfield illumination. This applies to the largest thin sections examined by biologists and geologists in transmitted light and the opaque, planar specimens examined by the materials scientist in reflected light. These needs were once well met by Leitz with their Panphot and Aristophot systems and to a lesser extent by Zeiss with their Ultraphot II.
Special Topic: Advanced Basics of Immunostaining and Antigen Retrieval
Authors: Jerome W Gray (Jay)
Published: March 2018

The ability to immunologically link microscopic tags to specific proteins has produced major advances in all forms of microscopy. Initially researchers needed to make and label their own antibodies. This required a good working knowledge of immunology. Today's labeled antibodies are readily available from a variety of vendors. Although this has greatly facilitated the expansion of immunolabeling techniques, it has also led to their use by researchers with little or no background in immunology.
Print Your Own Organs!
Authors: Carmichael Stephen W
Published: March 2018

Would you believe it might be possible to build organs using an ink-jet printer? In a remarkable pair of articles, Thomas Boland and his collaborators describe a modified printer that promises to be abie to do exactly that.

The first article of this pair describes the software and hardware to arrange cells in two dimensions, just as a printer arranges droplets of ink on a fiat piece of paper. The software that normally controls the position of a drop of ink is modified to position a drop containing one or two cells in suspension onto a substrate.
Atom Probes Leap Ahead
Authors: Kelly Thomas F , Gribb Amy A
Published: March 2018

Since early times, the collective understanding of our microscopic universe has been directly tied to the quality of our microscopies. This has been true from the advent of light microscopes through to modern electron microscopes. Indeed, if one is to work on a given scale, one must be able to “see” at that scale. At the beginning of the 21st century, human inquiry is focused on the atomic scale.
Microscopy At The Ends Of The Earth
Authors: Breger Dee
Published: March 2018

The first time you stand on the deck of a research icebreaker as it crunches its way through the Antarctic pack Ice, you're surprised at how many colors there are. Ice covers the sea everywhere you look; perhaps here and there an occasional gargantuan iceberg rises majestically above the pack. Everything between you and all three hundred and sixty degrees of the horizon is gently undulating under brilliant sunshine in unison with the sea swell. It's a January mid afternoon, the heart of the southern summer, and you're bundled up against the biting cold. You can't stop smillng.
Precision and Detection Limits for EDS Analysis in the SEM
Authors: Lifshin Eric , Gauvin Raynald
Published: March 2018

Microanalysis using an EDS on an SEM are sometimes asked whether two samples are of different composition, or if different regions in the same sample vary in composition, A best educated guess may be that differences of a few percent can be distinguished under optimized conditions that include favorable data collection times and count rates, stable instrument operation, and well prepared samples and standards that remain free of contamination. Another frequently asked question is whether it is possible to detect a given amount of a particular element in a sample.
Creating Pseudocolored Images in Photoshop
Authors: Sedgewick Jerry
Published: March 2018

The method for creating pseudocolor in Photoshop can be done in few steps, but the image will not be colored in the conventional way. The conventional means for producing pseudocolor comes by using a look up table (LUT). This LUT is an overlay for making a range of colors according to choices provided by the software. The colors are matched to levels of brightness and darkness in the image (grayscale pixel values), typically from a short to long wavelengths. In that scenario, violet colors are matched to the black and near-black pixels and red to those dose to absolute white. Blue, yellow, green and orange become the mid-range pixel values.
Ultra Low Voltage BSE Imaging
Authors: Steigerwald Michael DG
Published: March 2018

LEO's field emission scanning electron microscopes are all based an the “GEMINI” principle as shown in figure 1. In order to reduce aberrations and sensitivity to interfering stray-fields the electron optical column possesses a positively biased booster that shifts the energy of the primary electrons. The incident beam is focussed by a combination of a magnetic lens with an axial gap that avoids field leakage to the specimen and an electrostatic retarding lens formed by the beam booster together with the grounded pole piece cap. Shortly before the electrons hit the specimen they are decelerated down to the desired primary energy.
Techniques for Combinatorial and High-Throughput Microscopy Part 2: Automated Optical Microscopy Platform for Thin Film Research
Authors: Kim S-W , Sehgal A , Karim A , Fasolka MJ
Published: March 2018

As it is in traditional materials science, microscopy is a central tool for morphology characterization in combinatorial and high-throughput (C&HT) materials research. Indeed, micrographs are naturally amenable to C&HT studies, since they enable rapid visual screening and automated quantitative analysis by a plethora of well-tested image processing routines. In this article, we present a custom-built and cost-effective automated optical microscopy (AOM) platform designed for the C&HT analysis of gradient specimens. Gradient specimens progressively vary one or more parameters with position, presenting a multitude of experimental conditions within a single sample (see Part 1 of this series).
A Polarizing Microscope for Mapping Birefringent Objects in 3D Space
Authors: Shribak Michael , Oldenbourg Rudolf
Published: March 2018

The traditional polarizing microscope equipped with crossed linear polarizers shows a picture in which the image contrast of a birefringent object depends on both the amount of relative retardation induced by the object and the orientation of its principal axis. For example, if the orientation of the principal axis is parallel to one of the polarizers, then the birefringent object becomes invisible. For best visibility, the principal axis must be oriented at 45° to the polarizers. In addition, the image intensity of the object is proportional to the square of the sine of the relative phase shift between the ordinary and the extraordinary ray passing through the object. The addition of a waveplate as compensator to the optical train provides the opportunity to improve the contrast and measure the relative retardation, but the principal restrictions of orientation dependence and non-linear image contrast remains.
The Total Release Method for FIB In-Situ TEM Sample Preparation
Authors: Moore TM
Published: March 2018

In 1965, Gordon Moore forecast that the microprocessor industry would continually scale to smaller feature sizes and the number of transistors would double every 18 months. Scaling below the 100nm node, combined with the implementation of copper and low dielectric constant insulators to increase the processor speed, has produced the situation in which SEM inspection no longer offers suitable resolution to image key artifacts and structures. The transmission electron microscope (TEM), once considered more of a development tool, is now in the forefront for process control and failure analysis, especially for measurements such as the thickness of semiconductor device non-planar barrier and seed layers
The Application of Electron Microscopy Techniques to the Space Shuttle Columbia Accident Investigation
Authors: Shah Sandeep , Jerman Greg
Published: March 2018

The Space Shuttle Columbia was returning from a 16-day research mission, STS-107, with nominal system performance prior to the beginning of the entry interface into earth's upper atmosphere. Approximately one minute and twenty four seconds into the peak heating region of the entry interface, an off-nominal temperature rise was observed in the left main landing gear brake line. Nearly seven minutes later, all contact was lost with Columbia. Debris was observed periodically exiting the Shuttle's flight path throughout the reentry profile over California, Nevada, and New Mexico, until its final breakup over Texas. During the subsequent investigation, electron microscopy techniques were crucial in revealing the location of the fatal damage that resulted in the loss of Columbia and her crew.
TEM of Paraffin-Embedded H&E- Stained Sections for Viral Diagnosis (An Unusual Papovavirus Case)
Authors: Estrada Januario C , Angelica Selim M , Miller Sara E
Published: March 2018

Viral infections can be focal and therefore difficult to find by electron microscopy. In addition to sampling limitations, sometimes the only specimen available for examination is tissue that has already been prepared for light microscopy (LM). We have diagnosed a papovavirus infection in skin by embedding hematoxylin and eosin (H&E)-stained sections for ultrathin sectioning and transmission electron microscopy (TEM).

Immunosuppressed patients can have unusual infections or infections in unusual locations. These agents may be difficult to identify due to their not being suspected and incorrect tests being ordered.
Imaging of the Development and Therapeutic Response of an In Vivo Fungal Catheter Biofilm
Authors: Nett Jeniel , Andes David
Published: March 2018

The majority of human pathogens cause disease in a biofilm lifestyle. Biofilms are communities of cells that remain attached to a foreign surface and to each other. The organisms secrete and become embedded in an extracellular polysaccharide matrix. Biofilm infections occur most commonly on implanted medical devices and are quite recalcitrant to antimicrobial therapy. The most common device involved in these infections is the intravenous catheter. More than 5 million intravenous catheters are inserted into patients in the United States annually of which up to 10% become infected with biofilm producing pathogens.
Characterization of Solids from Oilfield Emulsions
Authors: Cloud Richard W , Ramsey Rebecca L , Pultz Robert A , Poindexter Michael K
Published: March 2018

Production of crude oil is generally accompanied by several other product phases, namely water, gas and solids. Pressure drops across chokes, concomitant gas evolution (due to pressure drops) and turbulence caused by various pipeline configurations can create difficult-to-resolve emulsions. Natural crude oil surfactants and solids exacerbate the problem further by migrating to the newly created oil-water interface and stabilizing the unwanted emulsions. Once the fluids arrive at the production facilities, a variety of vessels are employed to separate the oil, gas and water. Depending on the wettability of the solids, they will exit via one or both of the liquid phases. In a worse case scenario, the solids will accumulate at the oil-water interface.
Writing Nano-Scale Patterns on Insulators Using Variable Pressure Electron-Beam Lithography
Authors: Miller Floyd , Frey David
Published: March 2018

Electron-beam lithography offers very high resolution patterns without the need for masks. Systems based on electron microscopes offer entry into electron-beam lithography at reasonable cost. Such systems are becoming popular in research environments due to their versatility and reasonable cost.

While these systems work well they do have problems writing on insulating substrates. The insulating substrate causes charge to build up from the incident electron-beam. As the charge builds up on the surface of the insulator, the incident beam is distorted and moved in x and y. The result is a lack of positioning accuracy on the patterns as well as pattern distortion.
Bugscope: The Second Year Of A Sustainable Remote Microscope Project For K-12 Educational Outreach
Authors: Potter CS , Carragher B , Carroll L , Conway C , Grosser B , Hanlon J , Kisseberth N , Robinson S , Stone D , Thakkar U , Weber D
Published: March 2018

Bugscope is a second generation educational project in the World Wide Laboratory that provides web browser based control of scientific imaging instrumentation using the Internet. We had previously demonstrated web based remote access to sophisticated scientific imaging systems several years ago in the Chickscope project. The primary goal of the Bugscope project is to demonstrate that relatively low cost, sustainable access to an environmental scanning electron microscope (ESEM) can be made available to K-12 classrooms.
Odd Vibration Sources
Authors: Carvalho Tina (Weatherby)
Published: March 2018

Chasing sources of vibration seems to be a never-ending problem in microscopy. Here are the approaches we've taken to two different sources of vibration affecting our Hitachi S-800 FESEM. One of the first problems was with a window air conditioning unit in the room that was needed to augment our so called central system. The existing window unit vibrated the window, walls, and floor. One solution may have been to buy a split unit so that the compressor was outdoors, but there was a moratorium on buying new air conditioning units
On The Trail of the Fathers: The Serendipitous Santos
Authors: Alden Harry A , Galvis Alvaro E
Published: March 2018

I am a botanist, with an expertise in plant anatomy, specifically wood anatomy. In my capacity of mkroscopist for the Smithsonian Institution, I help answer research questions developed by curators, conservators, anthropologists and archaeologists. I am typically presented with a variety of materials that range from large, entire objects from museums to small, deteriorated, fragmentary samples from archaeological digs. Many of the requests center around the questions “What is it?” and “Where did it come from?” The answers to these questions help determine the traditional materials used by a culture and the distribution of these objects through trade and cultural exchange. Of the numerous requests that I receive, one or two each year tend to stand out as captivating examples of applied optical microscopy. The one that I would like to present in this article (along with my intern for the project - Alvaro Galvis) is the early Catholic statues (santos) from Chihuahua, Mexico and southern California.
Fostering LIMS Development Through Open Standards Part II - Ontologies and Business Process
Authors: Goodblatt Avrum
Published: March 2018

This is the second in the series of short articles about Laboratory Information Management Systems (LIMS). This installment will focus on two issues - looking at ontologies and at business process design. The goal is to demonstrate how LIMS is really a combination of several capabilities, and that although each capability should be looked at separately, they ultimately must all work together as seamlessly as possible.

Before diving in, I would like to thank Dr. Q. C. Yu, the director of our Biomedical Imaging Facility here in Pathology and Laboratory Medicine at Penn http://www.med.upenn.edu/bmcrc/morph/?morph for his assistance, encouragement, and sponsorship of my participation in the Honolulu conference.
Brief Review: Basic Properties and Applications of Carbon Nanotubes
Authors: Seraphin Supapan
Published: March 2018

The first publication on the Buckminsterfullerene carbon molecule (C60) was in 1985 by Kroto et al. [1]. Not much else happened right after that since samples of C60 were not available for further study. It was the discovery of Krätschmer and Huffman's group [2] in 1990 that really opened up the field. They found a method to produce C60 in gram quantity. This made it possible for researchers around the world to investigate C60 properties and further advanced the field of nanocarbon research. Establishing the existence of a third crystalline form of carbon is one of the most exciting fundamental discoveries in science to date.
Computationally Mediated Experimental Science
Authors: Zaluzec Nestor J
Published: March 2018

The problems being addressed by today's microscopists and microanalysts are becoming increasingly complex and data intensive. Thirty five years ago, many of us were challenged by the mere process of recording a spectral profile and then using the limited resources we had at hand to analyze the data to obtain quantitative results. Today, we have within our laptop computers the processing power of yesterday's supercomputers, however, computing power alone will not be sufficient to solve the next generation of problems.
High Resolution 3-D Fluorescence Microscopy: A Comparison of Confocal Laser Scanning Microscopy and a wide-Field Deconvolution Technique
Authors:   Scanalytics, Inc.
Published: March 2018

Advances in the biological sciences have given rise for the need to visualize microscopic structures of interest. As the requirement to see specific structure and sub-resolution details arise, investigators have turned to fluorescent probes to label and observe these details, which are often undetectable using conventional methods in light microscopy. Fluorescence microscopy offers many advantages for visualizing specific structure and sub-resolution details, which are often undetectable using transmitted light microscopy. Recent advances in fluorescent probe and microscope design, as well as imaging instrumentation designed for fluorescence applications, are now permitting life-science researchers to view details in regions of interest with increasing precision, accuracy, and resolution.
SEM History
Authors: Darley Jim
Published: March 2018

Manfred von Ardenne was an EM pioneer and the first to publish a complete concept of a scanning electron microscope. A German overseas newscast reported the death of Manfred von Ardenne on 28 May. During the 1930s he was involved in cathode ray work and later lived In East Germany and did significant cancer research. Not mentioned in the newscast was his conceptual development of the SEM in the late 1930s.

He outlined the underlying principles of SEM operation: an electron probe scanning a small region of [fie specimen, the emitled electrons are captured, amplified and time-sequentially displayed on a cathode ray tube. Magnification is the ratio between the areas scanned and displayed His was the fantastic notion of a microscope without a magnifying lens.
Hold-'Em In Place
Authors: Ross Kristen R , Berens Michael E
Published: March 2018

We've used gelled agarose to cover & hold monolayer cells in place when treatment leads to cell lifting. Low-gelling temperature agarose (Type VII) (Sigma A 4018 or A 0701) can be made as a 2% stock solution in “phosphate-buffered saline” (PBS) (boiled then kept at 42° C to remain liquid). The agarose can be stored at room temperature at this time, but must be boiled and melted again before use.
A Quick Note on Freeze-Fixing Tissue in Liquid Nitrogen
Authors: Oshel Philip
Published: March 2018

There are two possibilites for plunge freezing in LN2: one is “normal” liquid nitrogen -- as it comes from the dewar, the other is slush nitrogen.

If using liquid nitrogen without slush, then something like isopentane, ethane, or propane (ordinary cooking propane will do) must be used. The caveat is that using these liquid gases is a serious fire and explosion hazard, especially since liquid oxygen forms at liquid nitrogen temperatures, and dissolves into the liquid hydrocarbon. These gases can be used safely (1 have done so) but they take care and understanding of what's happening, and a safe place to dispose of the cryogen.
A Quick, Economical and Gentle Method for Applying Small Volumes of Solutions to Specimens on Glass Slides
Authors: Hasenkampf Clare
Published: March 2018

I use immunocytochemical detection schemes that employ the use of primary and secondary antibodies for either tissue sections or whole mount preparations in order to study the in situ distribution of proteins and labeled nucleic acids. As the antibodies are either laboriously generated, or represent costly purchases. I have sought a protocol that minimizes the volume of antibody solution needed. Additionally I need a protocol that involves a quick, thorough, and gentle application and removal of the antibody solutions (mm the specimen with no danger of the specimen drying out during the one or two hour incubations. After trying many various schemes 1 have settled into the use of a procedure which very effectively retains the antibody solution on the specimen without damaging the delicate sections or whole mounts, and which is easy to add and remove.
NetSEM - Remote SEM Control
Authors: Chand Gobal
Published: March 2018

NetSEM for LEO 400 series microscopes makes the remote control of an SEM over the internet or telephone line a reality. Unlike current commercially available remote control applications which duplicate a Windows session on a remote PC, NetSEM presents a customizable interface which is accessed via a Web browser and uses lossy compression techniques to optimize SEM image transfer over high, variable and low bandwidth connections.
Sham, Sam, And Bacterial Communication
Authors: van Hook Lee
Published: March 2018

A scanning acoustic microscope (SAM) - a nanomicrophone using a piezoelectric crystal, may be used to examine bacterial colonies, not just materials specimens to detect phonons and listen to propagating microfractures.

Since bacterial cell walls are rigid structures, they undergo mechanical distortions when channels open and dose. This causes them to squeak and pop, each channel having its own sound. Channels and receptor molecules are all of different sizes and shapes, and therefore deform the cell wall in unique ways. This means that each channel makes a unique (if faint) sound when it passes a molecule through itself and this activity can be delected, Transport rates of uptake and excretion for the various compounds car then be calculated trom the intensity of the sounds.
Fun with Photoshop
Authors: Carvalho Tina (Weatherby)
Published: March 2018

Image editing sofiware is making it possible for us as microscopists to digitally prepare our micrographs for output as working prints, figures for journals, slides, inclusion in reports, or as files for transmission via the Internet or World Wide Web. In the course of becoming familiar with various sofiware applications, I decided to have some fun colorizing and recombining some scanning electron micrographs. While this kind of frivolity has no place in the presentation of scientific data, learning to manipulate images in this silly way serves two purposes; both to bring humor into the steep learning curve, and to highlight the sobering fact that you can no longer believe what you see in print. Although we would all hate to admit it, there may be unscrupulous scientists in our midst, tempted to alter visual data to suit their needs. Having said that, let me now show you one way it can be done...!
Tips on Focusing Transmission Electron Microscopes
Authors: Chapman Steve
Published: March 2018

Recently, there was a thread on the microscopy listserver about focusing TEMs, in particular whether to focus at crossover, or at the illumination level used for recording images. When setting the image focus there are a number of problems that may complicate matters.
How do I Visualize a Thin Gold Film on a Smooth Surface
Authors: Mager Mary
Published: March 2018

A question on the Microscopy Listserver concerned using an FESEM to examine a thin, thermally-evaporated gold film on single crystal germanium. It is always a difficult problem to find small surface details or textures on a smooth surface in the SEM. A surface without visible topography looks the same whether it is in or out of focus, and so the method to make sure the surface is in focus is a slow, iterative one.

My researchers like to give me a one inch square of highly polished steel or titanium and ask me to find and analyze the five tiny inclusions somewhere in the middle. If there is a particular feature or area that I need to examine, I find that area by eye or under a low power, binocular light microscope and mark it with a fine, red felt-tip pen.
India Ink as a Tracer for Circulatory System Study in a Ganglion, With a Note on Using Ferritin, Lanthanum, and Horseradish Peroxidasefor the Blood-Brain Barrier
Authors: Buchanan JoAnn
Published: March 2018

Several summers ago, while working at the Marine Biological Laboratory in Woods Hole, Massachusetts, George Augustine (Duke University) and I wished to look at the circulation in the giant synapse of the squid, Loligo pealei. At that time, Dr. Eugene Copeland suggested the use of India ink in order to see the circulatory system. The ink contains carbon particles that are visible under the EM. In addition, it is visible to the naked eye.
Monitoring Electron Microscope Performance
Authors: Chapman Steve
Published: March 2018

It is most important that any test specimens used to audit an instrument are from a traceable source and are certified by a recognised body.

Traditional methods for the evaluation of resolution in the scanning electron microscope rely upon a high-density particle upon a low-density substrate, the most popular method being evaporated gold on a carbon substrate. Although most manufacturers use this method, it is subject to abuse as there is no inbuilt magnification standard and therefore the evaluation of the image may only be made through measurement. To simply judge the specimen by appearance as most scientists do, could lead to a misleading result.

An ideal specimen for the evaluation of scanning electron microscope performance is dried polystyrene latex sputter coated with gold, or gold palladium for the evaluation of higher performance (e.g., field emission instruments) (Figure1). The specimen requires very pure polystyrene latex that is allowed to settle and dry down over a period of time sufficient for it to form a solid block. The block is fixed to a specimen stub with silver Dag and the adhesive allowed to dry.
Really Tiny Tweezers
Authors: Carmichael Stephen W
Published: March 2018

Laser tweezers take advantage of the forces around converging beams of light to exert slight pressures on small structures. Whereas these optical devices have allowed for some elegant studies of cell biology, wouldn't it be great if we had mechanical tweezers that offered even better manipulation? In a recent paper, Philip Kim and Charles Lieber demonstrated a fabulous device they called “nanotweezers.“

Logically, they used nanotubes as the key structural component for their nanWith nanotubes serving as the tines of the tweezers, Kim and Lieber devised a very clever arrangement for the hub. They took a standard glass tube, 1 mm in diameter, and pulled it to a tapered end of about 100 nm.otweezers. Carbon nanotubes are particularly strong for their size, they conduct electricity, and they can be fabricated as small as 1 nanometer (nm) in diameter. With nanotubes serving as the tines of the tweezers, Kim and Lieber devised a very clever arrangement for the hub. They took a standard glass tube, 1 mm in diameter, and pulled it to a tapered end of about 100 nm. They then evaporated a very thin coat of chromium and then gold on one side, then rotated the rod 180° and deposited metal on the other side. Each coated side operated as an independent electrode.
Preparation and Use of Needles and Micropipets for Handling Very Small Particles
Authors: Teetsov Anna
Published: March 2018

To successfully isolate 1-100 μm samples for microscopical examination or analysis, one needs a good set of microtools, with the most essential being the needle and the micropipet. This paper will describe how to make them and how they are used to solve various sample preparation problems.
Photoshop Distilled: Basic Black and White Image Adjustment for Microscopists
Authors: Carvalho Tina (Weatherby)
Published: March 2018

Ready or not, digital imaging in the microscope lab is here to stay. While I am one of those fogies who insist that digital images are nowhere near as good as photographic prints, I've also bowed to the inevitable, and begun to find ways to assist clients in our multi-user facility with their digital imaging needs. We can acquire digital images from our FESEM, with a CCD camera on our EFTEM, from our light microscope with a CCD, and from a flatbed scanner. Clients use their images for image analysis, transport to others scientists via the Internet or World Wide Web, for reports, slides, overhead transparencies, and publication. Generally, these images need to be manipulated for use, just as one wouid manipulate a photographic print in the darkroom to correct any deficiencies in exposure or area of view.
Teaching Old Microscopes New Tricks
Authors: Carmichael Stephen W
Published: March 2018

There are many transmission electron microscopes (TEMs) that have provided years of reliable service and good images, but they lack the positioning systems that are standard on the newest microscopes. A precise digital positioning capability is essential for many quantitative stereological studies and relocating specific features on a grid. For many of the older TEMs, retrofitting them with a digital positioning system is not an option, or at least a very expensive upgrade. Now Martin Hohmann-Marriott, William Sharp, Robert Roberson, and Robert Blankenship have described the hardware and software that offer a second life to these older microscopes.
VisBio: a Flexible Open-Source Visualization Package for Multidimensional Image Data
Authors: Rueden Curtis T , Eliceiri Kevin W
Published: March 2018

Over the past few years there has been a dramatic improvement in microscopy acquisition techniques, in effective imaging modalities as well as raw hardware performance. As the microscopist's available tools become more sophisticated and diverse—e.g., time-lapse, Z sectioning, multispectra, lifetime, nth harmonic, polarization, and many combinations thereof—we face a corresponding increase in complexity in the software for understanding and interpreting the resultant data. With lifetime imaging, for example, it is overwhelming to study the raw numbers; instead, an exponential curve-fitting algorithm must be applied to extract meaningful lifetime values from the mass of photon counts recorded by the instrument.
BioImageXD - New Open Source Free Software for the Processing, Analysis and Visualization of Multidimensional Microscopic Images
Authors: Kankaanpää Pasi , Pahajoki Kalle , Marjomäki Varpu , Heino Jyrki , White Daniel
Published: March 2018

With the recent success of the human genome project, researchers must now discover biological functions of the tens of thousands of proteins encoded in the genome. Molecular cell biology and structural biology methods are required for this work.

Modern multidimensional bioimaging methods, such as laser scanning confocal microscopy and other light microscopic techniques, have emerged as a major research methodology in this new era of informational biology. These methods all produce vast amounts of digital information and require specialized computer software to process and analyze it. Several programs intended for this purpose have become available in recent years, but microscopists around the world frequently discover them unsuitable for many of their required tasks. The reasons for this are varied, and include: extensive bugs that take too long to fix, prohibitively high prices (also for updates and bug fixes), algorithms that are undisclosed and as such unacceptable for accurate scientific work, limited sets of features dispersed into separate “modules”, complex and difficult user interfaces, and lack of flexibility in adapting to specific research situations.
Novel Developments in High-frequency Micro-Ultrasound Imaging
Authors: Little Tom
Published: March 2018

With the mapping of the mouse genome, the growing sophistication in transgenic sciences creating complex mouse models of disease, and the demand to study disease in vivo, there has been a corresponding increase in the demand for and development of preclinical imaging modalities. Clinical ultrasound operating in the 2-12 MHz range is a well established clinical imaging modality, accounting for more than one-third of all imaging procedures performed in North America. The simplicity, ease of use, speed, and safety of ultrasound have led to its significant role in diagnosis, treatment assessment, follow-up, and guidance of therapy in clinical applications. Ultrasound imaging is used routinely in its B-Mode imaging mode to report on soft tissue structures. It's also used in its Doppler modes for the measurement of blood velocity in fast-flowing targets such as the cardiovascular system, in slow-flowing applications such as quantifying blood flow and in vascular architectures within tumors.
The Scanning of Colour and B&W Film and Photographs for Image Processing, Analysis and Archiving - On a Tight Budget
Authors: Morris Keith J
Published: March 2018

Despite the advent of the new PC based digital camera era, there is still a vast archive of film. The obvious thing to do is to scan film optically using a high resolution film scanner and to convert the image into a digital file for digital distribution, PC archiving, and image processing. The likes of NASA can easily afford the best $20k plus PMT drum scanners and pro flatbed scanners for their spaceflight photo archives. See some professional scanners at http://www.imacon.dk, http://www.aztek.com, http://graphics.kodak.com (Creo) and http://www.flatbed-scanner-review.org. You can download selections from the NASA digitised archive at http://grin.hq.nasa.gov.