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  • richardmitnick 5:10 am on November 15, 2017 Permalink | Reply
    Tags: , , Microscopy   

    From COSMOS: “Need a better microscope? Add mirrors” 

    Cosmos Magazine bloc

    COSMOS Magazine

    15 November 2017
    Andrew Masterson

    Anthony Van Leeuwenhoek’s first microscope, from the seventeenth century, looks nothing like a modern SPIM microscope, but both are products of a quest to improve optics. Stegerphoto.

    From pre-classical times onwards, it could be argued, lens-makers have been the unsung heroes of science.

    As early as 750 BCE the Assyrians were shaping lenses from quartz. From there, the history of optics both underpins and enables discovery in both the macro and micro worlds.

    Where would science be today had it not been for the patient work of myriad lens grinders and optics theorists, including Francis Bacon, Galileo, van Leeuwenhoek, right up to Roberts and Young – inventors in 1951 of photon scanning microscopy – and beyond?

    Even today, the quest for better, clearer, more detailed images from lenses continues apace, with the latest advance, declared in the journal Nature Communications, coming from the US National Institutes of Health and the University of Chicago.

    The images obtained by the combination of the new coverslip and computer algorithms show clearer views of small structures. Credit: Yicong Wu, National Institute of Biomedical Imaging and Bioengineering

    In this diagram, you can see how the mirrored coverslip allows for four simultaneous views. Credit: Yicong Wu, National Institute of Biomedical Imaging and Bioengineering

    A team of researchers, led by Hari Shroff, head of the National Institute of Biomedical Imaging and Bioengineering’s lab section on High Resolution Optical Imaging (HROI), report the solution to a mechanical problem in microscope optics that was, in a way, of their own making.

    Several years ago, Shroff and colleagues developed a new type of microscope that performed “selective plane illumination microscopy” or SPIM. These microscopes use light sheets to illuminate only sections of specimens being examined, thereby doing less damage and better preserving the sample.

    In 2013, Shroff’s team created a SPIM microscope that used two lenses instead of one, which improved image quality and depth perception, In 2016, a third lens was added, allowing improved resolution and 3D-imagery.

    A fourth lens would have boosted matters even more, but at this point van Leeuwenhoek’s twenty-first century heirs hit a snag.

    “Once we incorporated three lenses, we found it became increasingly difficult to add more,” says Shroff. “Not because we reached the limit of our computational abilities, but because we ran out of physical space.”

    Proximity was a real issue. Not only were the three lenses crowded together, but all had to be positioned extremely close to the sample being examined to allow the imaging goal – detailed views of structures within a single cell, say – to be achieved.

    In their new paper, Shroff and his colleagues reveal a solution to the problem that is nothing if not elegant. Rather than try to cram an extra lens in, they have put mirrors on the coverslip – the thin piece of glass that sits on top of the sample.

    The result – especially when coupled with new algorithms in the computerised back-end of a SPIM microscope – is better speed, efficiency and resolution.

    “It’s a lot like looking into a mirror,” Shroff explains. “If you look at a scene in a mirror, you can view perspectives that are otherwise hidden. We used this same principle with the microscope.

    “We can see the sample conventionally using the usual views enabled by the lenses themselves, while at the same time recording the reflected images of the sample provided by the mirror.”

    The addition of the tiny mirrors was not without its own problems. Every microscope raw image contains unwanted data from the source of illumination used to light up the sample. With three lenses, there are three sources of this interference; with mirrors added, these too are multiplied.

    Shroff, however, took this problem to computational imaging researcher Patrick La Riviere at the University of Chicago, who, with his team, was able to modify the processing software to eliminate the extra noise and further improve the signal.

    Francis Bacon, one thinks, would have approved.

    See the full article here .

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  • richardmitnick 3:34 pm on July 31, 2017 Permalink | Reply
    Tags: 3-D microscope gives Johns Hopkins scientists a clearer view, , , , , Microscopy,   

    From Hopkins: “3-D microscope gives Johns Hopkins scientists a clearer view” 

    Johns Hopkins
    Johns Hopkins University

    Jill Rosen

    Light-sheet technology allows researchers like Kavli Neuroscience Discovery Institute fellow Audrey Branch to observe how cells, ducts, or veins connect without damaging the cells in the sample Image credit: Will Kirk / Homewood Photography.

    Audrey Branch is trying to learn more about aging by studying old and young brains. Specifically, she’s interested in how cells connect to form memories and what might be going wrong with those connections when older people start to forget things.

    Until recently, getting at that question meant months of tedious specimen preparation. And even then, the very prep that made getting a glimpse of the brain’s core possible—slicing what’s already tiny into thousands of pieces—very likely destroyed the delicate connections the Johns Hopkins neuroscientist needed to see.

    That changed this spring when a new, three-dimensional microscope arrived at the university’s Homewood campus, a cutting-edge tool that not only condenses what had been months of work into just hours, but allows researchers unprecedented views of organs, tissue, and even live specimens.

    Just practicing with it, Branch knew it was a game-changer. She cried when she saw the first pictures of a mouse brain, its individual neurons glowing red, and its spindly dendrites, too—showing quite clearly the links between those cells.

    “It feels so amazing to see the brain in a way that no one has ever seen it before,” she said. “It’s pretty much the greatest thing I’ve ever experienced in science.”

    The selective plane florescence light sheet microscope arrived on campus in April, one of the first in operation on the East Coast and the only one in Maryland. Purchased with a grant from the National Institutes of Health, it cost $360,000.

    Unlike other microscopes, this one illuminates specimens from the side, shooting two perfectly aligned planes of light across an object, illuminating a wafer-thin slice of the whole while the camera captures the image—thousands of times over as the specimen moves through the light. When the images are displayed together, the result is a three-dimensional image or video clip of the full object, sort of like the more familiar CAT scan.

    The technology is very new, but Michael McCaffery, director of the university’s Integrated Imaging Center, expects researchers everywhere will be using it within a few years. Just among the Johns Hopkins community, word of the light sheet is already out and scientists have been lining up to use it—even if that requires the minor inconvenience of bringing specimens over from the medical campus.

    “People really want to use this,” McCaffery said. “It fills a niche that until now was unavailable at Hopkins. Simply, there was no instrument that allowed a researcher to take a whole organ, brain, or cardiac muscle, and image them in three-dimensions, in their entirety.”

    The light sheet is the latest advance in modern microscopy—a world that’s been evolving since fluorescence microscopy became the standard in the 1960s. Now, most researchers use confocal microscopes, which use lasers to illuminate a sample point by point—only extremely tiny samples will work—then create computerized images, pixel by pixel.

    Confocals produce vivid, high-resolution images, but the sample size limitations—nothing thicker than about 70 microns, which is about as wide as a strand of human hair—severely handicapped scientists.

    The new light sheet allows samples up to 12 to 15 millimeters, or about a half an inch. Researchers can study much larger samples, even entire organs. And because the samples don’t have to be cut up, researchers like Branch who are interested in how cells, ducts, or veins connect have a chance to observe them, unspoiled.

    “It’s a very big deal for researchers, particularly those interested in the science of connectomics,” McCaffery said. “Mapping the neuronal connections of the brain is the holy grail of neurology.”

    It’s certainly Branch’s holy grail.

    Branch is a Kavli Neuroscience Discovery Institute fellow working in the Krieger School of Arts and Sciences. She wants to know how newborn neurons, which are key to making memories, connect to other cells in the brain—and how those connections might change as people age.

    Scientists know the number of newborn neurons declines with age, and that likely has something to do with why short-term memory declines with age. What Branch wants to do is audit these newborn cells in a young brain, determining how many there are, where they are, and what other cells they communicate with. She can compare that with an older brain and possibly see which connections have broken when memory loss occurs. If she can target the broken connections, there could be a way to treat the area with a drug and stop or slow cognitive decline.

    Branch has been practicing on the light sheet with mouse brains, and she plans to formally investigate her hypothesis with rat brains, which are bigger and more human-like.

    If she didn’t have the light sheet, Branch would have to slice the brain, which is about the size of an olive pit, into tissue-thin sections—about 250 pieces. Each slice would need to be stained, mounted onto a slide, and then imaged. Each of those images would need to be manually assembled into a composite to approximate the whole.

    All of this work would take about a month. Since Branch’s experiment involves 30 brains, it would take her about two and a half years, “if,” she says, “that’s all I did day in and day out.”

    Worse yet, by slicing the brain, she would lose most of the newborn neurons she needed to find, and probably all of the connections. She figures if she had marked 50 newborn neurons, she’d be lucky to find five.

    “It would be impossible to find the connections,” she says. “And it would be impossible to get an idea of who each of those cells is talking to. Maybe it’s not important, but I’m guessing that’s not the case. Neurons in isolation aren’t interesting; it’s who they’re talking to, it’s how they’re wired.

    “I was just going to have to estimate. I’d have missed a lot of the picture, and that’s all anyone’s been able to do.”

    Guy Bar-Klein, a neuroscientist working in the Hal Dietz Lab at the School of Medicine, has been crossing town to spend time at Homewood’s Dunning Hall with the light sheet to study blood vessels in the heart and brain, hoping to better understand what causes aneurysms.

    Without the light-sheet technology, his view would be limited to a minuscule section of tissue, much too small to get a true sense of its vasculature. Now, he has been looking at samples with intact blood vessels, making it possible to spot and track aneurysms—and possibly pinpoint the underlying issues that caused it to form.

    “It’s very exciting,” Bar-Klein said. “I think it gives us a very substantial advantage in understanding the signaling involved in aneurysm formation.”

    Michael Noë, a pathology resident who studies pancreatic cancer, hopes the light sheet’s three-dimensional perspective will allow him to see relationships between tumors and the surrounding nerves and blood vessels. Tumors often grow around nerves, and Noë expects the new perspective of cancerous ducts and nerves could shed light on why.

    “For almost 200 years, pathologists looked at tissue the same way,” he says. “Three-dimensional is almost a whole new world for us. There is a lot of excitement in the department of pathology to apply this technology for the first time to human samples.”

    Before researchers can view tissue of any sort with the light-sheet, their samples must be treated to make them translucent, so the microscope’s light can pass through and create an image. Noë has developed a protocol for clearing human tissue and tumors, work he’s hoping to publish.

    Branch expects to have 3-D images of all 30 of her rat brains in three to six months.

    She’ll see every newborn neuron. She’ll see each dendrite. And hopefully, she’ll find answers – she already knows she’ll find more questions.

    “The technology makes it easier to have confidence about our findings,” she says, “It also opens up an opportunity to ask even more questions — things that before, we didn’t even know we could ask.”

    See the full article here .

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    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

  • richardmitnick 6:50 am on July 12, 2016 Permalink | Reply
    Tags: , Microscopy, , UW researchers improve microscopy method to ‘swell’ cellular structures bringing fine details into view   

    From U Washington: “UW researchers improve microscopy method to ‘swell’ cellular structures, bringing fine details into view” 

    U Washington

    University of Washington

    July 11, 2016
    James Urton

    Cellular biologists work at a frustratingly small scale. Like their colleagues in particle physics, these scientists investigate fundamental questions about our lives and our world — but at a scale beyond the skill of our primate eyes. Microscopes have helped bring this erstwhile invisible world into focus — and over the past several centuries since their invention, advances in microscopy have helped scientists visualize many details of life on the cellular level. But these approaches have costs — expensive equipment and complex specimen treatments — that ultimately restrict their widespread use.

    Microscopy also has its limit. Light’s inherent wavelike behavior limits any microscope’s resolving power. The most minute details of our existence — from twisted strands of DNA to bulbous cellular organelles — are difficult or impossible for even the best and most expensive microscopes to visualize directly.

    In this rat kangaroo kidney call, bundles of tubulin protein strands (green) snag on to chromosomes (blue) as the cell prepares to divide. Joshua Vaughan

    But scientists from the University of Washington recently reported a relatively simple method that would allow ordinary laboratory microscopes to illuminate many of these cellular structures quickly and efficiently. They did not modify microscopes to boost resolution. Instead, they used an approach to swell the tiny, complex structures within cells, bringing them within range of a microscope’s existing resolving range.

    “This is a radically new way of doing microscopy,” said UW chemistry professor Joshua Vaughan, who is senior author on a paper detailing their approach in Nature Methods. “The focus had largely been on hardware — improving the resolution of microscopes. Here, we expand the cell’s interior to bring it into view.”

    Appropriately, this technique is known as expansion microscopy.

    “This is a simple and robust approach that is surprisingly effective,” added Vaughan.

    His team was inspired by the expansion approach developed at the Massachusetts Institute of Technology. The MIT researchers stained cells with a complex, DNA-based fluorescent probe that would make cellular contents visible. They then treated cells with an expandable polymer that linked to the custom probes and would “inflate” the specimens to as much as four times their original size. But, this approach was laborious, and required specialized, expensive reagents.

    “When I saw their approach, I thought it was amazing,” said Vaughan. “But we were wondering if there was a way to do this using simpler staining strategies and conventional probes. That would make expansion microscopy accessible to thousands of labs.”

    Instead of complex fluorescent probes, Vaughan’s team turned to conventional fluorescent dyes bound to antibodies, which are easier to use, and developed a simple chemical treatment that would allow the antibodies to become linked to the polymer. They then treated their stained samples — slices of mammalian brain tissue and cultured cells — with the expandable polymer as well as enzymes that could create small “snips” in proteins to help them expand.

    Zooming in to a mammalian kidney cell, long strands of tubulin proteins before (top) and after (bottom) expansion treatment, showing the improved resolution of expansion microscopy.Joshua Vaughan

    They used this basic approach to come up with two staining protocols for expansion microscopy — one that worked better for individual cells and another for slices of tissue. Under the microscope, their images showed substantially brighter stains while maintaining excellent resolution. As an added bonus, their approach also enables expansion microscopy with fluorescent proteins, another popular fluorescent probe used by biologists. Critically, the UW team was able to obtain these high-resolution images on conventional, widely used laboratory microscopes.

    “We think this will make expansion microscopy a widely used technique for researchers who want to visualize what they’re studying with a relatively simple, low-cost approach that also has excellent performance,” said Vaughan.

    Vaughan said he hopes that other research groups will modify his team’s basic approach for other organisms or cell types, especially structures like cell walls that would resist expansion. Given the details illuminated by expansion microscopy, a hidden world awaits.

    Two scientists from the UW Department of Chemistry, doctoral student Tyler Chozinski and postdoctoral researcher Aaron Halpern, were co-first authors on the paper. Other authors were postdoctoral researcher Haruhisa Okawa and professor Rachel Wong — both in UW Medicine’s biological structure department — and UW undergraduates Hyeon-Jin Kim and Grant Tremel. The work was funded by the National Institutes of Health, the National Science Foundation, the Burroughs-Wellcome Fund and the University of Washington.

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

  • richardmitnick 3:00 pm on September 18, 2015 Permalink | Reply
    Tags: , Microscopy, ,   

    From MIT: “Extending super-resolution techniques” 

    MIT News

    Department of Physics graduate student Takuma Inoue built the super-resolution microscopy set up in the Cissé lab at MIT to study single molecule behavior of enzyme clusters that enable gene copying and protein production within living cells. On the table, five different lasers excite different fluorescent proteins at different wavelengths and image their location.

    Photo: Denis Paiste/Materials Processing Center

    Overcoming limitations of super-resolution microscopy to optimize imaging of RNA in living cells is a key motivation for physics graduate student Takuma Inoue, who works in the lab of MIT assistant professor of physics Ibrahim Cissé.

    Inoue, 26, was the first student to join Cissé’s lab at MIT in January 2014, and he built the lab’s super-resolution microscopy setup to study enzyme clusters that enable gene copying and protein production within living cells. Inoue, who this September enters his fourth year toward his PhD, originally started his experimental work in an atomic physics lab, where he worked on an imaging setup to trap extremely cold atoms in a vacuum. He is studying biophysics, atomic physics, and condensed matter physics.

    After learning that Cissé needed someone to set up his super-resolution microscopy, Inoue switched to Cissé’s lab. Because he did not have a biology background, Inoue says, “I wasn’t very much familiar with that, but the tools that you use and the methods for imaging are very common with what I had previously done. By building the setup, I got used to what things we can do in the lab. Then I made the transition to actually targeting some biomolecules within the cell to image and for me that was RNA.”

    “Initially, I had to start with building the microscope, which took me several months, and then I tried doing the continuation of his previous work which is imaging some kind of protein inside of a living cell,” Inoue says. “But then he gave (me) this project of RNA imaging as my main project for my PhD, because that will be more challenging, and we thought no one has ever achieved this big goal.”

    “My project makes sure that we overcome as many limitations as possible because there are different aspects of this for all the projects that we do,” Inoue adds. “There is the setup and there is this data analysis software and also we need to label the target molecules of interest properly. Each of them is, of course, not perfect. There are many challenges and limitations. But if you have a final goal in your project, I think you need to care about all of those different aspects and try optimizing. I’ve been doing experiments for a long time, so overcoming such limitations in the lab was one of my interests.”

    Inoue is developing techniques for easily tagging and visualizing RNA directly in living cells. “For me as an experimentalist, it’s a very exciting challenge to achieve the imaging of RNA within a live cell and to bring it to the level of a single molecule. My goal is achieve a technique to image single molecules of RNA inside of a living cell. That can have very broad applications. I think it’s very transformative,” Inoue says.

    The common approach to such imaging is genetic modification that adds a derivative of green fluorescent protein to the target of study — for example, RNA polymerase II. Inoue says his approach is to avoid genetic modification by developing oligonucleotide probes, which are short strands of genetic material that can bind to the target. “I try to deliver these probes into these natural cells and try to see if the target molecules get this fluorescence. And then I bring those cells to the imaging room and then do imaging,” he says. The technique is called fluorescent in situ hybridization. The oligonucleotide and the RNA target both start out as single strand molecules, but when they bind they can form a double helix like DNA, Inoue explains.

    “There already are approaches for looking at RNA inside dead cells. That’s I think the easy part,” Takuma’s mentor, Cissé, explains. “A handful of labs have also reported on promising ways of labeling RNA in living cells, but those require extensive genetic modifications. Takuma’s whole point is actually bringing new techniques for easily tagging and visualizing any arbitrary RNA, without genetic modification, and directly inside the living cell. And his preliminary demonstrations also, I think, look very promising.”

    Inoue has high hopes for the project. “This project is about labeling arbitrary RNA that exist inside a living cell, and I am at the developing stage of these techniques,” he says. “I’m hoping that through this project I can contribute and help many researchers in studying their RNAs of interest and also I, myself, am interested in studying different kinds of RNA.”

    The Cissé lab’s single molecule studies of the role that enzymes, proteins, and RNA play in gene expression is funded under National Institutes of Health Project No. 1DP2CA195769-01 with additional funds from the National Cancer Institute.

    The super-resolution imaging setup captures images through the microscope onto an electron-multiplying charge-coupled device (EM-CCD). “It can detect very sensitive signals, even single photons, and also it’s a very fast camera,” Inoue explains. The EM-CCD has millisecond exposure times but overall it takes several minutes to get one super-resolution image made from about 10,000 images.

    A native of Yokohama, Japan, Inoue moved to the U.S. at age 18, three years after his father, Hiroshi Inoue, accepted a position in Maryland starting up a life sciences subsidiary for Canon. Now a resident of Rockville, Maryland, Takuma Inoue received his bachelor’s in physics with a minor in mathematics at the University of Maryland at College Park, where his father currently holds the title of Professor of the Practice in Bioengineering.

    “I’ve got a lot of influence from my dad because he was initially an engineer, but then it was a very big surprise to me that he switched to biology and started doing some kind of engineering that could help biologists or could help people. So, that was maybe one of the key events in my life,” he says.

    “I like to think about scientific challenges and also there are many engineering challenges, and I really like that I am doing that, and also that I am trying to solve the world’s most interesting problems in the field of biology using my physics background. I want to see first how this project goes, and if possible, I’d like to continue doing research, and I hope that my career becomes exciting,” Inoue says.

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    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

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  • richardmitnick 1:53 pm on August 31, 2015 Permalink | Reply
    Tags: , , Microscopy   

    From Caltech: “New, Ultrathin Optical Devices Shape Light in Exotic Ways” 

    Caltech Logo

    Ker Than

    Schematic drawing of generation and focusing of radially polarized light by a metasurface. Credit: Dr. Amir Arbabi/Faraon Lab/Caltech

    Caltech engineers have created flat devices capable of manipulating light in ways that are very difficult or impossible to achieve with conventional optical components.

    The new devices are not made of glass, but rather of silicon nanopillars that are precisely arranged into a honeycomb pattern to create a “metasurface” that can control the paths and properties of passing light waves.

    These metasurface devices, described in a paper published online on August 31, 2015, in the journal Nature Nanotechnology, could lead to ultracompact optical systems such as advanced microscopes, displays, sensors, and cameras that can be mass-produced using the same photolithography techniques used to manufacture computer microchips.

    “Currently, optical systems are made one component at a time, and the components are often manually assembled,” says Andrei Faraon (BS ’04), an assistant professor of applied physics and materials science, and the study’s principal investigator. “But this new technology is very similar to the one used to print semiconductor chips onto silicon wafers, so you could conceivably manufacture millions of systems such as microscopes or cameras at a time.”

    Seen under a scanning electron microscope [SEM], the new metasurfaces that the team created resemble a cut forest where only the stumps remain. Each silicon stump, or pillar, has an elliptical cross section, and by carefully varying the diameters of each pillar and rotating them around their axes, the scientists were able to simultaneously manipulate the phase and polarization of passing light. Light is an electromagnetic field, and the field of single-color, or monochromatic, light oscillates at all points in space with the same frequency but varying relative delays, or phases.

    Scanning electron microscope

    Manipulating this relative delay, or phase, influences the degree to which a light ray bends, which in turn influences whether an image is in or out of focus.

    Polarization refers to the trajectory of the oscillations of the electromagnetic field at each point in space. Manipulating the polarization of light is essential for the operation of advanced microscopes, cameras, and displays; the control of polarization also enables simple gadgets such as 3-D glasses and polarized sunglasses.

    “Using our metasurfaces, we have complete control of the polarization and phase of light,” says study first author Amir Arbabi, a senior researcher at Caltech. “We can take any incoming light and shape its phase and polarization profiles arbitrarily and with very high efficiency.”

    While the same goal can be achieved using an arrangement of multiple conventional optical components such as glass lenses, prisms, spatial light modulators, polarizers, and wave plates, these many components lead to much bulkier systems. “If you think of a modern microscope, it has multiple components that have to be carefully assembled inside,” Faraon says. “But with our platform, we can actually make each of these optical components and stack them atop one another very easily using an automated process. Each component is just a millionth of a meter thick, or less than a hundredth of the thickness of a human hair. ”

    In addition to being compact, a metasurface device could manipulate light in novel ways that are very hard and sometimes impossible to do using current setups. For example, the Caltech team showed that one of their metasurfaces can project one image when illuminated by a horizontally polarized beam of light, and a different image when illuminated by a vertically polarized beam. “The two images will appear overlapped under illumination with light polarized at 45 degrees,” Faraon says.

    In another experiment, the team was able to use a metasurface to create a beam with radial polarization, that is, a beam whose polarization is pointing toward the beam axis. Such beams have doughnut-shaped intensity profiles and have applications in superresolution microscopy, laser cutting, and particle acceleration. “You generally would need a large optical setup, consisting of multiple components, to create this effect using conventional instruments,” Arbabi says. “With our setup, we can compress all of the optical components into one device and generate these beams with higher efficiency and more purity.”

    The team is currently working with industrial partners to create metasurfaces for use in commercial devices such as miniature cameras and spectrometers, but a limited number have already been produced for use in optical experiments by collaborating scientists in other disciplines.

    In addition, the Faraon lab current is investigating ways to combine different metasurfaces to create functioning optical systems and to correct for color distortions and other optical aberrations. “Like any optical system, you get distortions,” Faraon said. “That’s why expensive cameras have multiple lenses inside. Right now, we are experimenting with stacking different metasurfaces to correct for these aberrations and achieve novel functionalities.”

    The paper is entitled Dielectric metasurfaces for complete control of phase and polarization with sub wavelength spatial resolution and high transmission. In addition to Faraon and Arbabi, other Caltech coauthors include graduate student Yu Horie and Mahmood Bagheri, a microdevices engineer at JPL. The work was supported by the Caltech/JPL President’s and Director’s Fund and the Defense Advanced Research Projects Agency. Yu Horie was supported by the Department of Energy’s Energy Frontier Research Center program and a Japan Student Services Organization fellowship. The device nanofabrication was performed in the Kavli Nanoscience Institute at Caltech.

    See the full article here.

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 7:56 am on May 14, 2015 Permalink | Reply
    Tags: , , , Microscopy, , ,   

    From MIT: “Researchers build new fermion microscope” 

    MIT News

    May 13, 2015
    Jennifer Chu

    Graduate student Lawrence Cheuk adjusts the optics setup for laser cooling of sodium atoms. Photo: Jose-Luis Olivares/MIT

    Laser beams are precisely aligned before being sent into the vacuum chamber. Photo: Jose-Luis Olivares/MIT

    Sodium atoms diffuse out of an oven to form an atomic beam, which is then slowed and trapped using laser light. Photo: Jose-Luis Olivares/MIT

    A Quantum gas microscope for fermionic atoms. The atoms, potassium-40, are cooled during imaging by laser light, allowing thousands of photons to be collected by the microscope. Credit: Lawrence Cheuk/MIT

    The Fermi gas microscope group: (from left) graduate students Katherine Lawrence and Melih Okan, postdoc Thomas Lompe, graduate student Matt Nichols, Professor Martin Zwierlein, and graduate student Lawrence Cheuk. Photo: Jose-Luis Olivares/MIT

    Instrument freezes and images 1,000 individual fermionic atoms at once.

    Fermions are the building blocks of matter, interacting in a multitude of permutations to give rise to the elements of the periodic table. Without fermions, the physical world would not exist.

    Examples of fermions are electrons, protons, neutrons, quarks, and atoms consisting of an odd number of these elementary particles. Because of their fermionic nature, electrons and nuclear matter are difficult to understand theoretically, so researchers are trying to use ultracold gases of fermionic atoms as stand-ins for other fermions.

    But atoms are extremely sensitive to light: When a single photon hits an atom, it can knock the particle out of place — an effect that has made imaging individual fermionic atoms devilishly hard.

    Now a team of MIT physicists has built a microscope that is able to see up to 1,000 individual fermionic atoms. The researchers devised a laser-based technique to trap and freeze fermions in place, and image the particles simultaneously.

    The new imaging technique uses two laser beams trained on a cloud of fermionic atoms in an optical lattice. The two beams, each of a different wavelength, cool the cloud, causing individual fermions to drop down an energy level, eventually bringing them to their lowest energy states — cool and stable enough to stay in place. At the same time, each fermion releases light, which is captured by the microscope and used to image the fermion’s exact position in the lattice — to an accuracy better than the wavelength of light.

    With the new technique, the researchers are able to cool and image over 95 percent of the fermionic atoms making up a cloud of potassium gas. Martin Zwierlein, a professor of physics at MIT, says an intriguing result from the technique appears to be that it can keep fermions cold even after imaging.

    “That means I know where they are, and I can maybe move them around with a little tweezer to any location, and arrange them in any pattern I’d like,” Zwierlein says.

    Zwierlein and his colleagues, including first author and graduate student Lawrence Cheuk, have published their results today in the journal Physical Review Letters.

    Seeing fermions from bosons

    For the past two decades, experimental physicists have studied ultracold atomic gases of the two classes of particles: fermions and bosons — particles such as photons that, unlike fermions, can occupy the same quantum state in limitless numbers. In 2009, physicist Marcus Greiner at Harvard University devised a microscope that successfully imaged individual bosons in a tightly spaced optical lattice. This milestone was followed, in 2010, by a second boson microscope, developed by Immanuel Bloch’s group at the Max Planck Institute of Quantum Optics.

    These microscopes revealed, in unprecedented detail, the behavior of bosons under strong interactions. However, no one had yet developed a comparable microscope for fermionic atoms.

    “We wanted to do what these groups had done for bosons, but for fermions,” Zwierlein says. “And it turned out it was much harder for fermions, because the atoms we use are not so easily cooled. So we had to find a new way to cool them while looking at them.”

    Techniques to cool atoms ever closer to absolute zero have been devised in recent decades. Carl Wieman, Eric Cornell, and MIT’s Wolfgang Ketterle were able to achieve Bose-Einstein condensation in 1995, a milestone for which they were awarded the 2001 Nobel Prize in physics. Other techniques include a process using lasers to cool atoms from 300 degrees Celsius to a few ten-thousandths of a degree above absolute zero.

    A clever cooling technique

    And yet, to see individual fermionic atoms, the particles need to be cooled further still. To do this, Zwierlein’s group created an optical lattice using laser beams, forming a structure resembling an egg carton, each well of which could potentially trap a single fermion. Through various stages of laser cooling, magnetic trapping, and further evaporative cooling of the gas, the atoms were prepared at temperatures just above absolute zero — cold enough for individual fermions to settle onto the underlying optical lattice. The team placed the lattice a mere 7 microns from an imaging lens, through which they hoped to see individual fermions.

    However, seeing fermions requires shining light on them, causing a photon to essentially knock a fermionic atom out of its well, and potentially out of the system entirely.

    “We needed a clever technique to keep the atoms cool while looking at them,” Zwierlein says.

    His team decided to use a two-laser approach to further cool the atoms; the technique manipulates an atom’s particular energy level, or vibrational energy. Each atom occupies a certain energy state — the higher that state, the more active the particle is. The team shone two laser beams of differing frequencies at the lattice. The difference in frequencies corresponded to the energy between a fermion’s energy levels. As a result, when both beams were directed at a fermion, the particle would absorb the smaller frequency, and emit a photon from the larger-frequency beam, in turn dropping one energy level to a cooler, more inert state. The lens above the lattice collects the emitted photon, recording its precise position, and that of the fermion.

    Zwierlein says such high-resolution imaging of more than 1,000 fermionic atoms simultaneously would enhance our understanding of the behavior of other fermions in nature — particularly the behavior of electrons. This knowledge may one day advance our understanding of high-temperature superconductors, which enable lossless energy transport, as well as quantum systems such as solid-state systems or nuclear matter.

    “The Fermi gas microscope, together with the ability to position atoms at will, might be an important step toward the realization of a quantum computer based on fermions,” Zwierlein says. “One would thus harness the power of the very same intricate quantum rules that so far hamper our understanding of electronic systems.”

    Zwierlein says it is a good time for Fermi gas microscopists: Around the same time his group first reported its results, teams from Harvard and the University of Strathclyde in Glasgow also reported imaging individual fermionic atoms in optical lattices, indicating a promising future for such microscopes.

    Zoran Hadzibabic, a professor of physics at Trinity College, says the group’s microscope is able to detect individual atoms “with almost perfect fidelity.”

    “They detect them reliably, and do so without affecting their positions — that’s all you want,” says Hadzibabic, who did not contribute to the research. “So far they demonstrated the technique, but we know from the experience with bosons that that’s the hardest step, and I expect the scientific results to start pouring out.”

    This research was funded in part by the National Science Foundation, the Air Force Office of Scientific Research, the Office of Naval Research, the Army Research Office, and the David and Lucile Packard Foundation.

    See the full article here.

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  • richardmitnick 10:40 am on May 8, 2015 Permalink | Reply
    Tags: , , , , Microscopy   

    From AAAS: “Electron microscopes close to imaging individual atoms” 



    7 May 2015
    Robert F. Service

    This composite image of the protein β-galactosidase shows the progression of cryo-EM’s ability to resolve a protein’s features from mere blobs (left) a few years ago to the ultrafine 0.22-nanometer resolution today (right). Veronica Falconieri/ Subramaniam Lab/CCR/ NCI/ NIH

    Today’s digital photos are far more vivid than just a few years ago, thanks to a steady stream of advances in optics, detectors, and software. Similar advances have also improved the ability of machines called cryo-electron microscopes (cryo-EMs) to see the Lilliputian world of atoms and molecules. Now, researchers report that they’ve created the highest ever resolution cryo-EM image, revealing a druglike molecule bound to its protein target at near atomic resolution. The resolution is so sharp that it rivals images produced by x-ray crystallography, long the gold standard for mapping the atomic contours of proteins. This newfound success is likely to dramatically help drugmakers design novel medicines for a wide variety of conditions.

    “This represents a new era in imaging of proteins in humans with immense implications for drug design,” says Francis Collins, who heads the U.S. National Institutes of Health in Bethesda, Maryland. Collins may be partial. He’s the boss of the team of researchers from the National Cancer Institute (NCI) and the National Heart, Lung, and Blood Institute that carried out the work. Still, others agree that the new work represents an important milestone. “It’s a major advance in the technology,” says Wah Chiu, a cryo-EM structural biologist at Baylor College of Medicine in Houston, Texas. “It shows [cryo-EM] technology is here.”

    Cryo-EM has long seemed behind the times—an old hand tool compared with the modern power tools of structural biology. The two main power tools, x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, enable researchers to pin down the position of protein features to less than 0.2 nanometers, good enough to see individual atoms. By contrast, cryo-EM has long been limited to a resolution of 0.5 nm or more.

    Cryo-EM works by firing a beam of electrons at a thin film containing myriad copies of a protein that have been instantly frozen in place by plunging them in liquid nitrogen. Detectors track the manner in which electrons scatter off different atoms in the protein. When an image is taken, the proteins are strewn about in random orientations. So researchers use imaging software to do two things; first, they align their images of individual proteins into a common orientation. Then, they use the electron scattering data to reconstruct the most likely position of all the protein’s amino acids and—if possible—its atoms.

    Cryo-EM has been around for decades. But until recently its resolution hasn’t even been close to crystallography and NMR. “We used to be called the field of blob-ology,” says Sriram Subramaniam, a cryo-EM structural biologist at NCI, who led the current project. But steady improvements to the electron beam generators, detectors, and imaging analysis software have slowly helped cryo-EM inch closer to the powerhouse techniques. Earlier this year, for example, two groups of researchers broke the 0.3-nm-resolution benchmark, enough to get a decent view of the side arms of two proteins’ individual amino acids. Still, plenty of detail in the images remained fuzzy.

    For their current study, Subramaniam and his colleagues sought to refine their images of β-galactosidase, a protein they imaged last year at a resolution of 0.33 nm. The protein serves as a good test case, Subramaniam says, because researchers can compare their images to existing x-ray structures to check their accuracy. Subramaniam adds that the current advance was more a product of painstaking refinements to a variety of techniques—including protein purification procedures that ensure each protein copy is identical and software improvements that allow researchers to better align their images. Subramaniam and his colleagues used some 40,000 separate images to piece together the final shape of their molecule. They report online today in Science that these refinements allowed them to produce a cryo-EM image of β-galactosidase at a resolution of 0.22 nm, not quite sharp enough to see individual atoms, but clear enough to see water molecules that bind to the protein in spots critical to the function of the molecule.

    That level of detail is equal to the resolution of many structures using x-ray crystallography, Chiu says. That’s vital, he adds, because for x-ray crystallography to work, researchers must produce millions of identical copies of a protein and then coax them to align in exactly the same orientation as they solidify into a crystal. But many proteins resist falling in line, making it impossible to determine their x-ray structure. NMR spectroscopy doesn’t require crystals, but it works only on small proteins. Cryo-EM represents the best of both worlds: It can work with massive proteins, but it doesn’t require crystals.

    As a result, the new advances could help structural biologists map vast numbers of new proteins they’ve never mapped before, Chiu says. That, in turn, could help drug developers design novel drugs for a multitude of conditions associated with different proteins. But one thing the technique has already shown is crystal clear, that in imaging, as well as biology, slow, evolutionary advances over time can produce big results.

    See the full article here.

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  • richardmitnick 5:11 am on January 20, 2015 Permalink | Reply
    Tags: , Microscopy,   

    From Yale: “New laser could upgrade the images in tomorrow’s technology” 

    Yale University bloc

    Yale University

    January 19, 2015
    Jim Shelton


    A new semiconductor laser developed at Yale has the potential to significantly improve the imaging quality of the next generation of high-tech microscopes, laser projectors, photo lithography, holography, and biomedical imaging.

    Based on a chaotic cavity laser, the technology combines the brightness of traditional lasers with the lower image corruption of light emitting diodes (LEDs). The search for better light sources for high-speed, full-field imaging applications has been the focus of intense experimentation and research in recent years.

    The new laser is described in a paper in the Jan. 19 online edition of the Proceedings of the National Academy of Sciences. Several Yale labs and departments collaborated on the research, with contributions from scientists in applied physics, electrical and biomedical engineering, and diagnostic radiology.

    “This chaotic cavity laser is a great example of basic research ultimately leading to a potentially important invention for the social good,” said co-author A. Douglas Stone, the Carl A. Morse Professor and chair of applied physics, and professor of physics. “All of the foundational work was primarily motivated by a desire to understand certain classes of lasers — random and chaotic — with no known applications. Eventually, with input from other disciplines, we discovered that these lasers are uniquely suited for a wide class of problems in imaging and microscopy.”

    One of those problems is known as “speckle.” Speckle is a random, grainy pattern, caused by high spatial coherence that can corrupt the formation of images when traditional lasers are used. A way to avoid such distortion is by using LED light sources. The problem is, LEDs are not bright enough for high-speed imaging.

    The new, electrically pumped semiconductor laser offers a different approach. It produces an intense emission, but with low spatial coherence.

    “For full-field imaging, the speckle contrast should be less than ~4% to avoid any disturbance for human inspection,” explained Hui Cao, professor of applied physics and of physics, who is the paper’s corresponding author. “As we showed in the paper, the standard edge-emitting laser produced speckle contrast of ~50%, while our laser has the speckle contrast of 3%. So our new laser has completely eliminated the issue of coherent artifact for full-field imaging.”

    Co-author Michael A. Choma, assistant professor of diagnostic radiology, pediatrics, and biomedical engineering, said laser speckle is a major barrier in the development of certain classes of clinical diagnostics that use light. “It is tremendously rewarding to work with a team of colleagues to develop speckle-free lasers,” Choma said. “It also is exciting to think about the new kinds of clinical diagnostics we can develop.”

    The first author of the paper is Brandon Redding. Additional authors included Alexander Cerjan, Xue Huang, and Minjoo Larry Lee.

    Redding and Cao designed, fabricated, and tested the new laser. Lee and Huang grew the laser’s semiconductor wafer via molecular beam epitaxy, and helped in fabrication and testing. Choma aided in the design and performance criteria for the laser, provided expertise in spatial coherence and speckle in imaging, and is working with Redding to apply the laser for full-field imaging at Yale School of Medicine. Stone and Cerjan modeled the laser and analyzed its characteristics.

    See the full article here.

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    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 5:51 am on August 2, 2014 Permalink | Reply
    Tags: , , Microscopy   

    From UC Berkeley: “CNR Purchases Powerful New Microscope” 

    UC Berkeley

    UC Berkeley

    August 1, 2014
    Karyn Houston

    A microscopy expert at UC Berkeley has won a grant to purchase an amazingly powerful new microscope that will enable scientists to study the tiniest of organisms.

    “This new microscope will enable researchers to see objects that are impossible to see using technology available at Berkeley today,” said Steve Ruzin, director of the Biological Imaging Facility, located on the UC Berkeley campus in Koshland Hall, in the College of Natural Resources.

    Ruzin is an expert in microscopes and his cutting-edge Biological Imaging Facilty serves thousands of faculty, students and staff. Not only are a wide variety of microscopes available for researchers to use, but the lab also teaches students and other researchers about microscopy, the technical field of using microscopes to view samples and objects that cannot be seen with the naked eye.

    “Cells have bustling shipping centers,” said Amita Gorur, a graduate student in the Randy Schekman Lab at UC Berkeley. “The Elyra PS.1 Super Resolution microscope will allow me to track and visualize cargo on a freight car moving along cellular rail roads from destination A to B in real time. These cellular shipping units are so small that only the resolution achieved by this microscope will allow us to see them. That’s powerful!”

    Flagella of Giardia


    Differentiating Objects from One Another


    The new $600,000 instrument, purchased with a National Institutes of Health grant, is a “Structured Illumination Microscope” that allows researchers to image and differentiate different parts of a cell, using different fluorescent dyes.

    “In microscopy, and any optical system, to ‘see’ something is the ability of the system (microscope, telescope, eye) to determine whether two closely spaced objects are, in fact, two objects or really only one larger object,” Ruzin said. This “limit of resolution” is determined by the wavelength of light that is used to illuminate the sample. The resolution limit was defined in the 1880s by the German scientist Ernst Abbe, and it is still valid today.

    “In practical terms this means that the smallest object that can be resolved in a light microscope is about one third of a micrometer, or 300 nanometers,” Ruzin said. To put that size into perspective:

    New Technology

    In the last few years three separate technologies have become available that overcome the limit of resolution. The new microscope uses one of these technologies called “Structured Illumination,” that illuminates the sample with a known pattern of light.

    The illumination pattern induces a complex light pattern that is emitted from the sample. Subsequent computer processing of the emitted pattern reveals sub-resolution structures within the sample. The new microscope will achieve a resolution of 100nm, and will be able to see objects that are 10 times smaller than a bacterium, or 10,000 times smaller than a period.

    Steve RuzinThis ability to resolve objects smaller than the theoretical limit is the reason a microscope like this is called a “Super-Resolution Microscope”. It will enable researchers to see:

    Arash Komeili’s lab in the Department of Plant & Microbial Biology is one of the many labs on campus that will benefit from the new instrument.

    The Komeili group studies magnetosomes, bacterial organelles 50-70 nm in diameter that control the formation of magnetic nanoparticles. Due to their small size and tight arrangement within the cell, conventional fluorescence microscopy cannot distinguish between individual magnetosomes.

    “We anticipate that the improved resolution of the Structured Illumination Microscope will allow us to study the dynamics of specific proteins at the individual magnetosome level,” Komeili said.

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

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  • richardmitnick 6:33 pm on June 30, 2014 Permalink | Reply
    Tags: , , Microscopy   

    From Argonne Lab: “Microscopy charges ahead” 

    News from Argonne National Laboratory

    May 28, 2014
    Jared Sagoff

    Ferroelectric materials – substances in which there is a slight and reversible shift of positive and negative charges – have surfaces that are coated with electrical charges like roads covered in snow. Accumulations can obscure lane markings, making everyone unsure which direction traffic ought to flow; in the case of ferroelectrics, these accumulations are other charges that “screen” the true polarization of different regions of the material.

    Ferroelectric materials are of special interest to researchers as a potential new form of computer memory and for sensor technologies.

    Argonne materials scientists Seungbum Hong (left) and Andreas Roelofs adjust an atomic force microscope.Photo credit: Wes Agresta/Argonne National Laboratory.

    In order to see this true polarization quickly and efficiently, researchers at the U.S. Department of Energy’s Argonne National Laboratory have developed a new technique called charge gradient microscopy. Charge gradient microscopy uses the tip of a conventional atomic force microscope to scrape and collect the surface screen charges.

    “The whole process works much like a snowplow scraping along the roads,” said Argonne materials scientist Seungbum Hong, who led the research. “Before, all we had was a snowshovel.”

    Ferroelectric materials are not usually polarized in any particular way, but they are rather the combination of different domains that are each polarized in different directions. “The end goal of the research is to be able to map these different regions quickly and accurately,” Hong said.

    “Until now, the process of trying to map these regions has been incredibly arduous and time-consuming,” added Argonne Nanoscience and Technology interim division director Andreas Roelofs, who came up with the idea for the study. “What was taking us 10 to 15 minutes now takes seconds.”

    Previous efforts in this arena had focused on the application of a different kind of microscope using piezoresponse force microscopy (PFM). In this technique, an applied voltage causes a small displacement of atoms in the material, generating a noticeable mechanical effect, or vibration. In reverse, the same phenomenon is responsible for the workings of the lighters in gas grills.

    The problem with PFM is that it is very slow and requires sophisticated equipment to measure a tiny motion of the material. “Before, we had to sit on one spot for a long time to get enough signal to understand how the material moves because we could just barely sense it,” Roelofs said. “For the past 15 years or so, we’ve tried to increase the speed of the measurements and made only modest progress while adding a lot of complexity.”

    “Now, everyone can use a standard tool to do this work much more cheaply and efficiently,” he added.

    An article based on the study appears in the April 23 early edition of the Proceedings of the National Academy of Sciences.

    This research was funded by the U.S. Department of Energy’s Office of Science.

    See the full article here.

    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

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