imaging

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Heartbeats under magnetic resonance imaging.

We seldom consider the force with which our hearts beat through every moment of our lives. Most of us will only ever feel the dampened strength of these muscles at the arteries of the wrist or neck, perhaps through a stethoscope or in moments of excitement, exertion and fear. Take a moment to consider it now, if you will. 

Credit to the VCU Medical Center for these images.

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New Technique Lets Scientists See Through Whole Organisms

by Michael Keller

Seeing is believing when it comes to understanding how organisms work. For biologists trying to learn about what’s going on inside a body, one of the biggest obstacles is not being able to put their eyeballs on a part or system without other objects getting in the way. The answer is usually going in with one invasive tool or another, which ends up damaging or destroying the thing they’re trying to investigate. 

Now California Institute of Technology scientists say they have improved upon a solution to clearing up the picture. The technique builds on work that garnered widespread attention last year. In that effort, assistant professor of biology Viviana Gradinaru and her team used detergent and a polymer to make a rodent brain transparent for study in unprecedented detail. 

Keep reading

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Real Time 3D LIDAR

Demonstration of LIDAR laser imaging tech developed by Heikki Hyyti features two rotating sensors working simultaneously. The video embedded below shows a data capture using the device whilst moving:

Sensor fusion with inertial and LIDAR data to estimate the position and velocities in real time. The current 3D point cloud is compared to the previous one to reduce errors caused by the integration of noisy and uncertain inertial measurements. The visualization shows two adjacent 3D point clouds on top of each other as the device, attached to an all-terrain vehicle, is driven around a parking lot and a young forest. The color of point cloud is determined by its height. Higher points are colored more lighter and greener as lower points are brownish. The visualization uses open source Point Cloud Library (http://pointclouds.org/) to present 3D data.

Real time LIDAR tech is already used in various ways (one example is in Austrailia, robotic “shepherds” are being trialed to remotely check on cattle), but this is the first example I have seen online using this method.

A couple of much shorter video examples can be found here

Woman of 24 found to have no cerebellum in her brain!

A woman has reached the age of 24 without anyone realising she was missing a large part of her brain. The case highlights just how adaptable the organ is.

The discovery was made when the woman was admitted to the Chinese PLA General Hospital of Jinan Military Area Command in Shandong Province complaining of dizziness and nausea. She told doctors she’d had problems walking steadily for most of her life, and her mother reported that she hadn’t walked until she was 7 and that her speech only became intelligible at the age of 6.

Doctors did a CAT scan and immediately identified the source of the problem – her entire cerebellum was missing (see scan). The space where it should be was empty of tissue. Instead it was filled with cerebrospinal fluid, which cushions the brain and provides defence against disease.

The cerebellum – sometimes known as the “little brain” – is located underneath the two hemispheres. It looks different from the rest of the brain because it consists of much smaller and more compact folds of tissue. It represents about 10 per cent of the brain’s total volume but contains 50 per cent of its neurons.

Read more:
http://tinyurl.com/pbzvw9c

from Daily Anatomy

CT scan reveals mummified monk inside a 1000 year old Buddha-like statue.

The Chinese statue, made of gold-painted papier-mâché, was suspected to contain human remains, but researchers were surprised to find that the internal organs had been removed prior to mummification.

The scan was carried out by the Netherlands-based Drents Museum at the Meander Medical Centre in Amersfoort.

Photo credits: M. Elsevier Stokmans; Boeddhamummie (Drents Museum); MMC / Jan van Esch.

New fluorescent protein permanently marks neurons that fire

A new tool developed at the Howard Hughes Medical Institute’s Janelia Research Campus lets scientists shine a light on an animal’s brain to permanently mark neurons that are active at a particular time. The tool — a fluorescent protein called CaMPARI — converts from green to red when calcium floods a nerve cell after the cell fires. The permanent mark frees scientists from the need to focus a microscope on the right cells at the right time to observe neuronal activity.

Calcium-sensitive fluorescent molecules called GCaMP emit a fluorescent signal that indicates neural activity, and are useful for following the dynamics of neural networks. But their signal is temporary, and if researchers miss it because the microscope is not focused on the right spot in the brain, the information is lost. With CaMPARI, researchers can visualize neural activity beyond a microscope’s limited field of view, capturing a snapshot of neural activity across wide swaths of brain tissue. The new tool also enables scientists to visualize neural activity during more complicated behaviors than previous calcium indicators, because in many cases it can be used while animals move freely, rather than being confined to a dish or embedded in agar.

“The most enabling thing about this technology may be that you don’t have to have your organism under a microscope during your experiment,” says Loren Looger, a group leader and protein chemist at Janelia who engineers tools to study the brain. “So we can now visualize neural activity in fly larvae crawling on a plate or fish swimming in a dish.”

Looger, Eric Schreiter, and their colleagues report on CaMPARI and its ability to label active neural circuits in fruit flies, zebrafish, and mice in the February 13, 2015, issue of the journal Science.

Schreiter, a senior scientist in Looger’s lab, led the development of CaMPARI, working as part of Janelia’s Genetically-Encoded Neuronal Indicator and Effector (GENIE) project team. GENIE is an interdisciplinary team dedicated to engineering fluorescent sensors that facilitate the imaging of neuronal activity in living organisms. Project teams are like small start-up companies within Janelia and were created to tackle biological problems that require collaboration across multiple labs.

To make CaMPARI, the team started with a fluorescent protein called Eos. Eos emits a green fluorescence until it is exposed to violet light, which permanently alters the protein so that it fluoresces in red. “That was the perfect starting place,” says Schreiter. “That conversion from green to red gives us a permanent signal. So we just needed a way to couple that conversion to the activity that’s going on in the cell.” To do that, the scientists incorporated a calcium-sensitive protein known as calmodulin, which makes the color change dependent on the burst of calcium that accompanies neural activity. It’s the same domain that scientists added to fluorescent proteins to make calcium-responsive GCaMP sensors.

To find a useful protein that switches the color of its fluorescence only in the presence of both calcium and an activating violet light, the researchers made and screened tens of thousands of subtly different proteins. “When we finally got one that photoconverted more with calcium than without it, we knew we had a tool. We just needed to make it better to get it to the point where another neuroscientist could sit down and use it,” says first author Ben Fosque, a graduate student in the biochemistry and molecular biophysics program at the University of Chicago.

The team spent more than a year tweaking their protein – making it brighter and more responsive to calcium and ensuring that it would work in cells and then in living mice, fruit flies, and zebrafish. In the end, they had a tool that they named CaMPARI, which stands for calcium-modulated photoactivatable ratiometric integrator.

The need to use violet light in converting the protein’s fluorescence gives experimenters control over the time period during which neural activity is tracked. “Ideally, we can flip the light switch on while an animal is doing the behavior that we care about, then flip the switch off as soon as the animal stops doing the behavior,” Schreiter explains. “Then we’re capturing a snapshot of only the activity that occurs while the animal is doing that behavior.”

The scientists conducted a series of experiments to demonstrate CaMPARI’s effectiveness. In one set of experiments, they captured a snapshot of neuronal activity over the entire brain volume of a zebrafish during a ten-second period as it swam in a dish. Following the experiment, CaMPARI was red in motor neurons known to be involved in swimming, as well as other expected sets of neurons–consistent with observations made by other scientists during electrophysiology experiments. The activation patterns changed significantly when the researchers altered the temperature or turbulence of the water.

In fruit flies, the team used CaMPARI to identify neurons that were activated in response to specific odors. Here too, the observations were as expected based on previous experiments: CaMPARI indicated that different odors activated distinct sets of neurons in the flies’ antennal lobes. In a subsequent set of experiments, the researchers experimentally activated the neurons that directly responded to the odors, then looked for neurons elsewhere in the brain that subsequently turned red. Those experiments revealed neurons that Schreiter says may be secondary, tertiary, or even quaternary components to the olfactory circuits. Tracing a circuit from one neuron to the next is difficult under a microscope, the scientists say, because cell projections and their connections to other cells generally extend beyond the instrument’s field of view.

With ongoing development, the scientists expect future versions of CaMPARI will be more sensitive and reliable than the current tool. But Looger says it’s important to get CaMPARI into the hands of neuroscientists right away. “The idea is probably more powerful than the tool, as it stands right now,” he says. “We will definitely benefit from a couple hundred–hopefully a thousand–labs taking CaMPARI and seeing what they can do with it.”

To that end, the team has made the genetic plasmid encoding CaMPARI available through the plasmid repository Addgene; transgenic flies expressing CaMPARI are available through the Bloomington Drosophila Stock Center; and Janelia group leader Misha Ahrens is distributing CaMPARI-expressing zebrafish to researchers. Tools for introducing CaMPARI into mouse cells should be available soon, the scientists say.

CaMPARI fluorescence in a larval zebrafish brain showing active neurons (magenta) that were marked while the fish was swimming freely. Credit: Looger Lab, HHMI/Janelia

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Research Sheds Light on How Blood Stem Cells Take Root

A see-through zebrafish and enhanced imaging provide the first direct glimpse of how blood stem cells take root in the body to generate blood. Reporting online in Cell, researchers in Boston Children’s Hospital’s Stem Cell Research Program describe a surprisingly dynamic system that offers several clues for improving bone-marrow transplants in patients with cancer, severe immune deficiencies and blood disorders, and for helping those transplants “take.”

The steps are detailed in an animation narrated by senior investigator Leonard Zon, director of the Stem Cell Research Program and professor of stem cell and regenerative biology at Harvard Medical School.

Read more: http://www.laboratoryequipment.com/videos/2015/01/research-sheds-light-how-blood-stem-cells-take-root

New HDlive ultrasound creates a clear and colorful 3D image of a fetus in utero. Parents get an excellent view of their child-to-be and doctors are able to see details that let them more accurately assess the fetus’s health.

The technology creates a moveable virtual light source and uses advanced skin rendering techniques to create realistic color. The virtual light source casts shadows and creates definition, highlighting every detail, every bump and every fold.

The new technique makes conventional black-and-white ultrasound images look virtually flat.

Images courtesy of Dr. Bernard Beniot, Princess Grace Hospital, Monaco

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