Tag Archives: 3D

Internal cell structures revealed by powerful 3D microscopy technique

A new imaging technique called cryo-SR/EM can capture cells in unprecedented, 3D detail.

Image credits D. Hoffman et al., (2020), Science.

The insides of living cells are very cramped, busy, but fascinating places. Sadly, because they’re so small, we’ve never been able to take a proper look at what’s going on inside there.

However, a new technique that combines both optical and electron microscopy may allow us to do just that, and in very high detail to boot.

Zoomed in

“This is a very powerful method,” says Harald Hess, a senior group leader at the Howard Hughes Medical Institute’s Janelia Research Campus, US.

Cryo-SR/EM combines data captured from electron microscopy with high-resolution optical microscope imaging to create detailed 3D models of the inside of cells.

Separately, these two approaches are powerful but limited. Optical (or light) microscopes can easily differentiate between individual cell structures when fluorescent molecules are attached to them — this is known as super-resolution (SR) fluorescence microscopy. While it does provide a clear picture, SR fluorescence microscopy isn’t able to show all the proteins swishing about inside a cell at the same time, making it hard to see how different bits interact with everything else.

On the other hand, electron microscopy (EM) can ‘see’ virtually everything that’s happening inside a cell in very high detail, but it can be too powerful for its own sake. The wealth of features inside a cell, all seen in very high detail, can make it difficult to understand what you’re looking at.

The team worked to combine these two techniques into a single one that enhances their strengths while balancing out their respective limitations.

Cryo-SR/EM involves first freezing a cell or group of cells under high pressure; this step instantly freezes their internal activity without allowing for ice crystals to form (these can easily rupture cellular structures). Next, the samples are placed into a cryogenic chamber where they’re imaged in 3D using SR fluorescence microscopy. Finally, the samples are removed, embedded in resin, and viewed under an electron microscope (this paper used a powerful device developed in Hess’ lab). This step involves shooting a beam of ions at the cell, producing images of successively layers of the cell. A computer program is used to piece these images back together into a 3D reconstruction.

For the final step, all the data is pooled together, creating a very high-detail 3D model of the cell’s interior.

Techniques such as cryo-SR/EM promise to let us peek into natural systems that were previously just too tiny to spot — and they let us do so in extreme detail. One particularly-exciting possibility is that cryo-SR/EM will allow researchers to observe snapshots of cellular processes as they unfold, propelling forward basic science and its applications in fields such as genetic engineering, bioengineering, biochemistry, and medicine.

The paper “Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells” has been published in the journal Science.

The Brain.

The first 3D interactive brain is here to teach you all about how yours works

Wonderfully resourceful and frighteningly complex, the human brain took us from bashing sticks together in the stone age to a force of geological proportions. Now, you can explore its intricacies in a novel interactive platform dubbed 3D Brain.

The Brain.

Image credits Society for Neuroscience.

Naturally, researchers have been trying to unlock its secrets out for a long time now, and although there’s still more to discover, our understanding of the brain is deeper than ever. Knowledge on its own isn’t much use, however, if it doesn’t work its way into still-functioning brains. With that in mind BrainFacts.org, a “public information initiative of The Kavli Foundation, the Gatsby Charitable Foundation, and the Society for Neuroscience – global nonprofit organizations dedicated to advancing brain research,” has teamed up with the Wellcome Trust, a biomedical research charity based in London, UK, to create a very fun tool named “3D Brain” (link at the bottom of the article.)

It’s the first platform of its kind, devoted to giving anybody with an internet connection, no matter their background, a basic understanding of how our brain works and how it shapes our behavior, wants, and fears. It’s a pretty compelling pitch, one I couldn’t pass on when BrainFacts asked me to take a shot at 3D Brain and see if I like it.

Brain game

“BrainFacts.org is allowing visitors to get inside the brain, teaching us the eight key concepts we all need to know about how the brain works, showcasing a scientifically accurate, interactive 3D model of the brain that reveals internal structures,” says John Morrison, the site’s editor-in-chief.

It all starts with a dialogue-box tutorial — that can finish in literally two clicks — followed by an introductory bit of text next to a floating, 3D model of the human brain. The app looks good but unassuming at first, so much so that, I confess, I’ve skipped the tutorial instructions, relying on my PC-game-trained brain to handle the controls to Brain. Half an hour and a strongly-exercised Wernicke’s area later, I’m still finding out I own bits of brain I hadn’t even thought I needed before (like a Wernicke’s area).

This interactive environment is extremely easy to use. Point and click on anything you’re curious about, click and hold to rotate the whole thing. Any area you’re looking at will be highlighted while the rest of the brain turns transparent so you can have a proper look. On the off-chance that something is still in the way, or if you just want to see how everything fits together, a “structure isolation” bar at the bottom lets you push everything apart. Teachers, professors, or just those of us who love explaining things to others, will be happy to hear that the app also lets you annotate any point across the brain and take snapshots.

Left Cerebral Hemisphere.

Image credits Society for Neuroscience.

I haven’t had any difficulties despite blatantly ignoring the tutorial, though I recommend you go through it if you’re not particularly tech-savvy. The software also runs smoothly, so you won’t have to wait around to switch between areas of the brain.

Brain’s intuitive interface hides a comprehensive look at the brain’s major structures. The 3D model on which Brain relies looks really nice and the app offers enough information to pique your interest without getting overwhelming.

All in all, I really like 3D Brain. More seasoned brain connoisseurs might find the data a bit limited, but I’ve actually learned a lot from it despite only going through about one-third of all the content so far. The 3D model really helps anchor everything you learn to a particular brain area, making it easier to remember later on. Ultimately, poking around the brain and seeing bits and pieces turn transparent or fly away to reveal different structures was really good fun, and that’s a wonderful incentive for learning.

I’ve had a lot of “oh I didn’t know it does that” or “that’s a weird shape” moments toying around with the app, and that seems to be what the people behind it planned all along.

“The experiences we’ve created on BrainFacts.org nurture curiosity and embrace the latest, interactive ways of learning,” says Eric J. Nestler, MD, PhD, and president of the Society for Neuroscience. “By designing these dynamic resources we are better informing the community and engaging students with interactive information about basic and clinical brain research.”

So if you’re looking to spruce up your knowledge of the brain, are looking for an exciting something extra to bring to class, or just want know what a Wernicke’s area is and why you need one, 3D Brain is right down your alley.

[button url=”http://www.brainfacts.org/3d-brain” postid=”” style=”btn-success” size=”btn-lg” target=”_self” fullwidth=”false”]3D Brain[/button]


Sperm captured in 3D for the first time, reveals corkscrewing swimming [with video]

Scientists have finally managed to track sperm patterns in 3D, for the first time in history. Bless their gifted brains, this remarkable achievement revealed some interesting and unexpected things: some sperm swim in corkscrew patterns, while others are hyperactive and hectic.

Aydogan Ozcan, the sperm study leader, placed sperm on a silicon sensor chip and used red and blue light to track their movement and plot their trajectories in 3D.

“The vast majority of the sperm followed a “typical” path-more or less a straight line. But some swam in a helical, or corkscrew, pattern previously only hinted at by fuzzy microscope results. Other sperm were labeled “hyperactive” due to their jerky direction changes, which sometimes sent them careening in reverse.”, he explained.

So it isn’t really a mad dash to the finish line for the little sperm, it’s actually a wiggly tap dance for some of them.

The smallest 3D printer

Although they’ve been around for a while, 3D printers still manage to impress me with the quality and precission of the outputted models. Recently, another step in the popularization of this technology has been made by addressing its size once with the development of the world’s smallest 3D printer to date.

The smallest 3D printer comes from the Vienna University of Technology in Austria, where a team of mechanical and chemical engineers developed a working product the size of a carton of milk, and weighing in at only 1.5 kilograms. The prototype’s cost was only  €1,200, remarkably cheap for this kind of technology and size employed; of course, if mass produced the price would drop off significantly.

The 3D printer works through layer by layer tech, as simply put by it’s creators.

The basic principle of the 3D-printer is quite simple: The desired object is printed in a small tub filled with synthetic resin. The resin has a very special property: It hardens precisely where it is illuminated with intense beams of light. Layer for layer, the synthetic resin is irradiated at exactly the right spots. When one layer hardens, the next layer can be attached to it, until the object is completed. This method is called “additive manufacturing technology”. “This way, we can even produce complicated geometrical objects with an intricate inner structure, which could never be made using casting techniques”, Klaus Stadlmann explains. He developed the prototype together with Markus Hatzenbichler.

Applications for this kind of device are quite varied and almost limitless. It can be used in the medical industry, you could  print your own spare parts if you can’t find one available (the resolution of the 3D printer is so high that it beats any kind of mold tech fly high), and of course you could transpose something your mind cooked up in CAD into the 3D physical realm.

Illustration of where the new SDSS map data exists in space and time.

Astronomers plot largest 3D map of the Universe

Illustration of where the new SDSS map data exists in space and time.

Illustration of where the new SDSS map data exists in space and time.

Unveiled this past weekend, astronomers from the Sloan Digital Sky Survey have created a 3D map of the Universe using the light from 14,000 quasars, some of the brightest bodies in the universe, to illuminate gas clouds in regions of space some 11 billion light years away. From the study‘s abstract:

These features arise as the light from the quasar is absorbed by the intervening neutral hydrogen. This gives one-dimensional information about the fluctuations in the neutral hydrogen density along the line of sight to the quasar. When spectra of many quasars are combined, it allows one to build a three-dimensional image of the fluctuations in the neutral hydrogen density and thus infer the corresponding fluctuations in the matter density.

Previous attempts at creating a working 3D map of the Universe have been with successful results in the past, but they had only gone as far as plotting galaxies 7 billion light-years away from Earth. This new version goes far beyond anything previously attempted in distance and time, as it charts clouds of hydrogen as far as 11 billion light years.

Image courtesy of Sloan Digital Sky Survey

Image courtesy of Sloan Digital Sky Survey

Of course, it’s not like someone will be able to chart through these maps anytime soon, especially considering we’re having difficulties reaching infinitely closer points compared, like Mars, but these mapped out 3D representations will provide absolute invaluable insights towards the formation of the Universe, and help answer numerous puzzling questions astronomers have long been after, including the nature of dark energy.

“We’re looking for a bump in the data that may tell us how fast universe is expanding,” said cosmologist Anže Slosar of Brookhaven National Laboratory, one of the researchers who presented the map May 1 at the American Physical Society meeting in Anaheim, California. “We don’t have enough data to see the bump yet, but we expect to get there in a few years.”

Data for the map was scanned with the help of the Baryon Oscillation Spectroscopic Survey, or BOSS, which can analyze light from individual quasars. The team analyzed 14,000 of about 160,000 known quasars and by 2014 astronomers hope to have 50,000 or 60,000 quasar slices in their grips; enough data, they hope, to finally elaborate a meaningful hypothesis concerning the formation and fate of the Universe. The researchers also plan to release a proper 3-D representation of the data (instead of the 2-D images shown here) for the public by then.

Slice of the full map showing the density of hydrogen gas in the ancient universe. Blue represents little gas, while red represents dense clouds.

Slice of the full map showing the density of hydrogen gas in the ancient universe. Blue represents little gas, while red represents dense clouds.

New interactive military holographic 3D map by DARPA

DARPA’s Urban Photonic Sandtable Display (UPSD) creates color, real-time, 3D holographic displays with up to 12 inches of visual depth. (c) DARPA

Today’s military generals meet on battlefields that are no longer vast, empty fields waiting to be bathed in blood, but in crowded, urban settings which most of the time represent tactical nightmares. The Defense Advanced Research Projects Agency (DARPA) recently completed a five-year program called Urban Photonic Sandtable Display (UPSD) that creates a real-time, color, 360-degree 3D holographic display to assist battle planners who may experience such distress.

On the UPSD up to 20 participants can zoom in, freeze, rotate and interact with battle zones on the holographic map, which can be as large as 6 feet and have a visual depth of 12 inches. No word on when the product will officially be deployed yet, only know is that the research and development phase of the product is over, conducted by Zebra Imaging of Austin via their won 2005 contract with DARPA.

Although most probably it is a very expensive product, I’m curious about its civilian applications. Business men and architects I’m sure would be all over the place on this one if they had the chance to purchase it. It’s still not Star Wars, but we’re getting there one step at a time.

Check out a video of Zebra Imaging testing out some low tech, first generation 3D holographic displays.

3D structure of humans finally decoded


It’s quite obvious that genetics is the most important step in our evolution that we have to take and although the molecular structure of DNA has been discovered more than half a century ago, its three dimensional structure remained a mystery. However, recently a team led by researchers from Harvard University, the Broad Institute of Harvard and MIT and the University of Massachusetts Medical School managed to solve this puzzle, paving the way for new insights into genomic functions and greatly expanding our understanding limits.

In order to accomplish this task, they employed a novel technology they call Hi-C and found out how DNA folds; the goal was to find out how our cells can somehow store three billion base pairs of DNA without having any of its functions blocked or impaired.

“We’ve long known that on a small scale, DNA is a double helix,” says co-first author Erez Lieberman-Aiden, a graduate student in the Harvard-MIT Division of Health Science and Technology and a researcher at Harvard’s School of Engineering and Applied Sciences and in the laboratory of Eric Lander at the Broad Institute. “But if the double helix didn’t fold further, the genome in each cell would be two meters long. Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter. This new approach enabled us to probe exactly that question.”

It has to be said, this Hi-C technology is almost as amazing as the discovery itself, at least from where I’m standing. To be able to go to such a level that allows assessment of the three dimensional interactions between DNA is just amazing. Regarding the importance of ‘decoding’ the structure, it basically means scientists will be able to find out how to turn most genes on and off:

“Cells cleverly separate the most active genes into their own special neighborhood, to make it easier for proteins and other regulators to reach them,” says Job Dekker, associate professor of biochemistry and molecular pharmacology at UMass Medical School and a senior author of the Science paper.

At an even finer scale, scientists had to reach out for mathematics, because DNA takes a shape of what is called in mathematics a ‘fractal‘. The specific architecture they found was named a ‘fractal globule’ that allows the cell to pack DNA unbelievable tightly. Just so you can make an idea, the density of information stored there is trillions and trillions of times bigger than that of the world’s best computer chip.


“Nature’s devised a stunningly elegant solution to storing information — a super-dense, knot-free structure,” says senior author Eric Lander, director of the Broad Institute, who is also professor of biology at MIT, and professor of systems biology at Harvard Medical School.

The idea of such a structure has in fac been suggested a while back, but it was as good as any guess at the moment, with no proof to back it up. However, thanks to this new kind of technology, the amazing truth was observed and scientists were able to solve the puzzle.

“By breaking the genome into millions of pieces, we created a spatial map showing how close different parts are to one another,” says co-first author Nynke van Berkum, a postdoctoral researcher at UMass Medical School in Dekker’s laboratory. “We made a fantastic three-dimensional jigsaw puzzle and then, with a computer, solved the puzzle.”

Zooming in on Mars: 3d pictures of the red planet

Get your 3D pictures on and join the show; hundreds of amazing pictures made by the HiRISE camera on NASA’s Mars Reconnaissance Orbiter (MRO) have been made, and despite the fact that this is not the first mission to take 3D pictures, HiRISE is by far the most powerful camera to do this, due to the significant progress in the field. We’re not going to show you all the pictures but instead, we have the best 5 pictures from NASA.

The Terby crater is 174 km wide and hydrated minerals show it may have once held an enormous lake, that was 3.6 km deep

The Terby crater is 174 km wide and hydrated minerals show it may have once held an enormous lake, that was 3.6 km deep

These wind eroded ridges have fascinated scientists for more than 3 decades

These wind eroded ridges have fascinated scientists for more than 3 decades

These dunes are on the floor of Herschel Crater, an impact basin from the ancient southern mountains of Mars; their shape is a result of the wind that blows mostly in only one direction

These dunes are on the floor of Herschel Crater, an impact basin from the ancient southern mountains of Mars; their shape is a result of the wind that blows mostly in only one direction

This steep depression is a bit more than 800 km long and it's one of the two large canyons that form the Valles Marineris canyon system which is the largest canyon in the SOLAR SYSTEM

This steep depression is a bit more than 800 km long and it forms the Valles Marineris canyon system, the largest canyon in the SOLAR SYSTEM

Invisibility: another sci-fi dream come true?

Invisible Man
Photo by Firentzesca

Recently, attempts to make “cloaking technology” possible have reached a great level, with major break throws. Among mentionable achievements, more notable are the work of Oleg Gadomsky, a Russian professor that managed to redirect light around objects and that of the people from the University of Maryland, who reported the successful cloaking of small 2D objects from all light waves.

Now, Scientists have created two new types of materials that can bend light the wrong way, creating the first step toward an invisibility cloaking device. The people behind this major achievement are the researchers at the Nanoscale Science and Engineering Center at the University of California, Berkeley, being the first to manage to cloak 3D materials.

One approach uses a type of fishnet of metal layers to reverse the direction of light, while another uses tiny silver wires, both at the nanoscale level. Both are so-called metamaterials — artificially engineered structures that have properties not seen in nature, such as negative refractive index.

The materials were developed by two separate teams, both under the leadership of Xiang Zhang of the Nanoscale Science and Engineering Center at the University of California, Berkeley with U.S. government funding. One team reported its findings in the journal Science and the other in the journal Nature.

Don’t treat the issue too seriously though. We’re a long way from witnessing the presence of invisible people on the street or the cloaking of whole buildings. Far from it. Here’s what Jason Valentine, one of the members of the projects, had to say.

“We are not actually cloaking anything,” Valentine said in a telephone interview. “I don’t think we have to worry about invisible people walking around any time soon. To be honest, we are just at the beginning of doing anything like that.”Valentine’s team made a material that affects light near the visible spectrum, in a region used in fiber optics.

“In naturally occurring material, the index of refraction, a measure of how light bends in a medium, is positive,” he said.

“When you see a fish in the water, the fish will appear to be in front of the position it really is. Or if you put a stick in the water, the stick seems to bend away from you.”

Fishnet On the left is the conceptual rendered “fishnet” design for the second cloaking material. The actual produced material is seen on the right in an electron microscope picture. It is capable of bending light backwards.

What’s a negative index of refraction, you ask?

“Instead of the fish appearing to be slightly ahead of where it is in the water, it would actually appear to be above the water’s surface,” Valentine said. “It’s kind of weird.”

For a metamaterial to produce negative refraction, it must have a structural array smaller than the wavelength of the electromagnetic radiation being used. Some groups managed it with very thin layers, virtually only one atom thick, but these materials were not practical to work with and absorbed a great deal of the light directed at it.

“What we have done is taken that material and made it much thicker,” Valentine said.

His team, whose work is reported in Nature, used stacked silver and metal dielectric layers stacked on top of each other and then punched through with holes. “We call it a fishnet,” Valentine said.

Immediate applications might be superior optical devices, Valentine said — perhaps a microscope that could see a living virus.

“However, cloaking may be something that this material could be used for in the future,” he said. “You’d have to wrap whatever you wanted to cloak in the material. It would just send light around. By sending light around the object that is to be cloaked, you don’t see it.”