bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sham, Sam, And Bacterial Communication
Authors: van Hook Lee 
Published: March 2018

Abstract
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

Abstract
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...!
How do I Visualize a Thin Gold Film on a Smooth Surface
Authors: Mager Mary 
Published: March 2018

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
Flies in a Box
Authors: Connelly Patricia S , Ruggiero Linda 
Published: March 2018

Abstract
A challenge was presented to us to find a way to support Drosophila melanogaster so that both the anterior and posterior scutellars could be easily visualized under a dissecting microscope and photographed for purpose of measurement. The resulting solution was to utilize a standard grid box with the lid removed. Several holes were filled with Gary's Magic Mountant to just above the rim of the hole. Freshly dead fruitflies were gently lifted with forceps. Then each was placed into a filled hole and both the head and abdomen were pushed into the mountant. The wings were arranged on the plastic on either side of the hole as seen in the micrographs.
The best results were obtained if the body of the fly was evenly covered with Gary's Magic Mountant and if the photography was accomplished within a few hours of the death of the fly.
Electron Tomography
Authors: Carmichael Stephen W 
Published: March 2018

Abstract
The transmission electron microscope (TEM) was invented in the 1930's, and developments in specimen preparation in the 1950's led to its widespread use as a tool to study structure in biologic systems. Similar in principle to the light microscope, but utilizing a much shorter wavelength for better resolution, the TEM has the image-forming beam pass through the specimen. This results in a two-dimensional image which can be difficult to interpret because features from different depths of the three dimensional specimen are superimposed. Traditionally this was dealt with by cutting sections of plastic-embedded specimens so thin (in the 40 to SO nanometer range) that they effectively had only two dimensions. To allow biologists to examine structures in three dimensions, serial sections are stacked and structures reconstructed. Even though computers have made reconstruction easier, the reality is that resolution in the depth dimension is limited by the section thickness. The technique of electron tomography is emerging as a way to overcome this limitation.
A 90-Degree-Tilt Rotary Adapter for SEM
Authors: Ehrman James M , Kaczmarska Irena 
Published: March 2018

Abstract
Many SEM stages prevent effective examination of specimens at extremely high tilt angles. Stage tilt may not be allowed at or near 90 degrees, and the design of the stage may cause the loss of X or Y stage motion at high tilts. We designed an adapter for our microscope that solves both problems by shifting the normal stage rotation motion 90 degrees (Figure 1). Specimen stubs are mounted horizontally in the adapter, and all components of the holder except the base plate are tethered to a stationary portion of the stage. Operation of the stage rotation control then rotates the stub around its horizontal axis (similar to a rotisserie). Specimens can be rotated through 360 degrees along this axis, with a full range of X and Y stage movement. A limited amount of stage tilt is also possible, allowing precise positioning of the specimen.
Measuring Conductivity With Scanning Probe Microscopes
Authors: Kalinin Sergei 
Published: March 2018

Abstract
There are two kinds of conductivity measurements possible with scanning probe microscopy (SPM). In the first case, the specific resistance of material directly below the tip is probed. In the second case, SPM probes local potential induced by the lateral current applied through macroscopic contacts, thus providing the information on the mesoscopic transport properties of the sample.
The first set of techniques is invariably based on measuring tip-surface current in contact or intermittent tapping mode. If the tip-surface contact resistance is small (good contact), the current will be limited by the spreading resistance of the sample from which specific resistance can be calculated, assuming that the contact area is known.
Adobe Photoshop® 6.0 Distilled: Preparation of Micrographs for Publication
Authors: Carvalho Tina Weatherby 
Published: March 2018

Abstract
A picture is said to be worth a thousand words; in the different fields of microscopy pictures are often our data as well. We interpret, analyze, and share images with our colleagues, and so image preparation, enhancement and presentation are crucial for this process. As image acquisition in microscopy moves away from capture on photographic film in favor of digital imaging methods, digital manipulation of visual data for presentation requires learning to use computer software tools. Adobe Photoshop, currently the standard in the community of both artists and scientists, is a powerful program, but it is NOT specifically designed for scientific data, and so contains dozens of features and tools that may and/or must be avoided in the preparation of micrographs for scientific publication. The learning curve for this type of software can be steep, but the steps outlined below may help to get you started.
The Emergence of Aberration Correctors for Electron Lenses
Authors: Silcox John 
Published: March 2018

Abstract
In 1936, Otto Scherzer published his famous theoretical paper on the correction of aberrations in round magnetic electron lenses. For fundamental reasons, the aberration coefficients are positive and to introduce negative corrections, the electron optical elements have to produce either charges or poles on the optic axis, or contain a mirror or be a multipole system. In 1997, three papers appeared with actual demonstrations of the correction of aberrations in imaging lenses, probe forming lenses and electron mirrors. It took almost two thirds of a century for this seemingly straightforward development to occur and for the promise of wavelength limited electron imaging to emerge as a practical proposition.
All That Glitters is not Gold: Approaches to Labeling for EM
Authors: Albrecht RM , Meyer DA 
Published: March 2018

Abstract
A large number of natural and synthetic species ranging from virus particles to small polymer beads have been employed over trie years as labels in electron microscopic applications. Perhaps the most useful and versatile of these labels are the colloidal heavy metals. The colloidal labels can be synthesized as round regular spheres in sizes from 1 to 150 nanometers in diameter and thus can be used where molecular and sub-molecular ranges of spatial resolution are required. They are electron “dense” and good emitters of secondary and back-scattered electrons and hence are readily detectable in both scanning electron microscopic imaging systems and transmission electron imaging systems. Larger particles, 10nm and above, can be identified via their shape in force based imaging systems.
Spectral Image Analysis: Getting The most from all That Data
Authors: Kotula PG , Keenan MR , Loehman R 
Published: March 2018

Abstract
How do you comprehensively analyze the chemistry of a microstructure with an SEM equipped with an energy-dispersive x-ray spectrometer (EDXS)? Prior to the 1990's there would have been perhaps two distinct and commercially available solutions to this problem. Firstly, you could have collected a number of point spectra each with a large number of counts and individually analyzed each one. The positive aspect of this, in principle, is that for each point the elemental correlations are maintained (e.g., a given point contains Al and O). The potential problem is that the region of the point analysis in question is not representative of the microstructure as a whole or subtle differences between different points could be missed. Additionally, point analyses are quite subjective and prone to missing potentially important regions of the microstructure.
Optical Projection Tomography
Authors: Carmichael Stephen W , Boppart Stephen A 
Published: March 2018

Abstract
There are many approaches to obtaining high-resolution images and three dimensional volumetric data sets, but all have limitations. Many techniques involve reconstructing volumes of information from sections, either physical sections or optical sections. Recently, James Sharpe, Ulf Ahlgren, Paul Perry, Bill Hill, Allyson Ross, Jacob Hecksher-Sørensen, Richard Baldock, and Duncan Davidson have developed an optical technique that is analogous to computed tomography (CT). Whereas clinical CT involves an X-ray source and detector rotating around the patient, optical projection tomography (OPT) has the specimen rotating within an optical pathway.
In situ Generation of Ruthenium Tetroxide and Osmium Tetroxide for the Physical Sciences and Their Reaction Indicators
Authors: Beauregard Paul 
Published: March 2018

Abstract
Recently, there was a suggestion on the MSA listserver about the use of osmium tetroxide (OsO4 and how to handle it. One suggestion was that ampoules be scored, placed in a glass jar, and the ampoule smashed to release the contents. This seemed like a very unsafe way to use osmium tetroxide or ruthenium tetroxide. The purpose of this article is to suggest a way to generate smaller amounts of these compounds in a safer manner than smashing ampoules and wondering about what to do with the unused portion after staining or storing. Another purpose is to discuss a new reaction indicator for mainly osmium tetroxide. The use of a reaction specific indicator was mandatory for judging the level or degree to which staining had proceeded in thin sections for the transmission electron microscope (TEM).
Use Adobe Acrobat to Keep Original Resolutions and to Make TIFF files from any Program
Authors: Sedgewick Jerry 
Published: March 2018

Abstract
The use of electronic files made universally readable in Adobe Acrobat will eventually replace paper submission in nearly every avenue used by scientists, whether files go to grants agencies, to reviewers, to colleagues via e-mail, or to publishers. It's for the obvious reason of reducing paper and the costs of mailing, but also because fonts often misbehave when going across operating system platforms, and because seemingly everyone has the Acrobat Reader, A better understanding of Adobe Acrobat can go a long way toward reducing the frustration that can easily arise from using this program inappropriately and ending up with poor image resolution.
Diffracted Light Contrast: Improving the Resolution of a Basic Light Microscope by an Order of Magnitude
Authors: Barry Piekos W 
Published: March 2018

Abstract
The discovery that the diffracted light from a convex edge can be used to form a very high-quality, shadowcast image on any light microscope has led to a device and method, diffracted-light contrast (DLC), which will allow shadowcast imaging to be routinely performed on student/laboratory microscopes (Piekos, 1999, 2003). The surface lattice of Surirella gema was easily resolved, and micrographs comparing the subcellular details of buccal epithelial cells viewed with DLC vs. Nomarski DIC showed that, on the microscopes used, DLC was superior in both the detail it rendered and depth of field. Although the images presented revealed DLC to be an excellent technique, the full capabilities of the technique were not known at the time.