Tag Archives: project
#431424 A ‘Google Maps’ for the Mouse Brain ...
Ask any neuroscientist to draw you a neuron, and it’ll probably look something like a star with two tails: one stubby with extensive tree-like branches, the other willowy, lengthy and dotted with spindly spikes.
While a decent abstraction, this cartoonish image hides the uncomfortable truth that scientists still don’t know much about what many neurons actually look like, not to mention the extent of their connections.
But without untangling the jumbled mess of neural wires that zigzag across the brain, scientists are stumped in trying to answer one of the most fundamental mysteries of the brain: how individual neuronal threads carry and assemble information, which forms the basis of our thoughts, memories, consciousness, and self.
What if there was a way to virtually trace and explore the brain’s serpentine fibers, much like the way Google Maps allows us to navigate the concrete tangles of our cities’ highways?
Thanks to an interdisciplinary team at Janelia Research Campus, we’re on our way. Meet MouseLight, the most extensive map of the mouse brain ever attempted. The ongoing project has an ambitious goal: reconstructing thousands—if not more—of the mouse’s 70 million neurons into a 3D map. (You can play with it here!)
With map in hand, neuroscientists around the world can begin to answer how neural circuits are organized in the brain, and how information flows from one neuron to another across brain regions and hemispheres.
The first release, presented Monday at the Society for Neuroscience Annual Conference in Washington, DC, contains information about the shape and sizes of 300 neurons.
And that’s just the beginning.
“MouseLight’s new dataset is the largest of its kind,” says Dr. Wyatt Korff, director of project teams. “It’s going to change the textbook view of neurons.”
http://mouselight.janelia.org/assets/carousel/ML-Movie.mp4
Brain Atlas
MouseLight is hardly the first rodent brain atlasing project.
The Mouse Brain Connectivity Atlas at the Allen Institute for Brain Science in Seattle tracks neuron activity across small circuits in an effort to trace a mouse’s connectome—a complete atlas of how the firing of one neuron links to the next.
MICrONS (Machine Intelligence from Cortical Networks), the $100 million government-funded “moonshot” hopes to distill brain computation into algorithms for more powerful artificial intelligence. Its first step? Brain mapping.
What makes MouseLight stand out is its scope and level of detail.
MICrONS, for example, is focused on dissecting a cubic millimeter of the mouse visual processing center. In contrast, MouseLight involves tracing individual neurons across the entire brain.
And while connectomics outlines the major connections between brain regions, the birds-eye view entirely misses the intricacies of each individual neuron. This is where MouseLight steps in.
Slice and Dice
With a width only a fraction of a human hair, neuron projections are hard to capture in their native state. Tug or squeeze the brain too hard, and the long, delicate branches distort or even shred into bits.
In fact, previous attempts at trying to reconstruct neurons at this level of detail topped out at just a dozen, stymied by technological hiccups and sky-high costs.
A few years ago, the MouseLight team set out to automate the entire process, with a few time-saving tweaks. Here’s how it works.
After injecting a mouse with a virus that causes a handful of neurons to produce a green-glowing protein, the team treated the brain with a sugar alcohol solution. This step “clears” the brain, transforming the beige-colored organ to translucent, making it easier for light to penetrate and boosting the signal-to-background noise ratio. The brain is then glued onto a small pedestal and ready for imaging.
Building upon an established method called “two-photon microscopy,” the team then tweaked several parameters to reduce imaging time from days (or weeks) down to a fraction of that. Endearingly known as “2P” by the experts, this type of laser microscope zaps the tissue with just enough photos to light up a single plane without damaging the tissue—sharper plane, better focus, crisper image.
After taking an image, the setup activates its vibrating razor and shaves off the imaged section of the brain—a waspy slice about 200 micrometers thick. The process is repeated until the whole brain is imaged.
This setup increased imaging speed by 16 to 48 times faster than conventional microscopy, writes team leader Dr. Jayaram Chandrashekar, who published a version of the method early last year in eLife.
The resulting images strikingly highlight every crook and cranny of a neuronal branch, popping out against a pitch-black background. But pretty pictures come at a hefty data cost: each image takes up a whopping 20 terabytes of data—roughly the storage space of 4,000 DVDs, or 10,000 hours of movies.
Stitching individual images back into 3D is an image-processing nightmare. The MouseLight team used a combination of computational power and human prowess to complete this final step.
The reconstructed images are handed off to a mighty team of seven trained neuron trackers. With the help of tracing algorithms developed in-house and a keen eye, each member can track roughly a neuron a day—significantly less time than the week or so previously needed.
A Numbers Game
Even with just 300 fully reconstructed neurons, MouseLight has already revealed new secrets of the brain.
While it’s widely accepted that axons, the neurons’ outgoing projection, can span the entire length of the brain, these extra-long connections were considered relatively rare. (In fact, one previously discovered “giant neuron” was thought to link to consciousness because of its expansive connections).
Images captured from two-photon microscopy show an axon and dendrites protruding from a neuron’s cell body (sphere in center). Image Credit: Janelia Research Center, MouseLight project team
MouseLight blows that theory out of the water.
The data clearly shows that “giant neurons” are far more common than previously thought. For example, four neurons normally associated with taste had wiry branches that stretched all the way into brain areas that control movement and process touch.
“We knew that different regions of the brain talked to each other, but seeing it in 3D is different,” says Dr. Eve Marder at Brandeis University.
“The results are so stunning because they give you a really clear view of how the whole brain is connected.”
With a tested and true system in place, the team is now aiming to add 700 neurons to their collection within a year.
But appearance is only part of the story.
We can’t tell everything about a person simply by how they look. Neurons are the same: scientists can only infer so much about a neuron’s function by looking at their shape and positions. The team also hopes to profile the gene expression patterns of each neuron, which could provide more hints to their roles in the brain.
MouseLight essentially dissects the neural infrastructure that allows information traffic to flow through the brain. These anatomical highways are just the foundation. Just like Google Maps, roads form only the critical first layer of the map. Street view, traffic information and other add-ons come later for a complete look at cities in flux.
The same will happen for understanding our ever-changing brain.
Image Credit: Janelia Research Campus, MouseLight project team Continue reading
Posted in Human Robots
#431377 The Farms of the Future Will Be ...
Swarms of drones buzz overhead, while robotic vehicles crawl across the landscape. Orbiting satellites snap high-resolution images of the scene far below. Not one human being can be seen in the pre-dawn glow spreading across the land.
This isn’t some post-apocalyptic vision of the future à la The Terminator. This is a snapshot of the farm of the future. Every phase of the operation—from seed to harvest—may someday be automated, without the need to ever get one’s fingernails dirty.
In fact, it’s science fiction already being engineered into reality. Today, robots empowered with artificial intelligence can zap weeds with preternatural precision, while autonomous tractors move with tireless efficiency across the farmland. Satellites can assess crop health from outer space, providing gobs of data to help produce the sort of business intelligence once accessible only to Fortune 500 companies.
“Precision agriculture is on the brink of a new phase of development involving smart machines that can operate by themselves, which will allow production agriculture to become significantly more efficient. Precision agriculture is becoming robotic agriculture,” said professor Simon Blackmore last year during a conference in Asia on the latest developments in robotic agriculture. Blackmore is head of engineering at Harper Adams University and head of the National Centre for Precision Farming in the UK.
It’s Blackmore’s university that recently showcased what may someday be possible. The project, dubbed Hands Free Hectare and led by researchers from Harper Adams and private industry, farmed one hectare (about 2.5 acres) of spring barley without one person ever setting foot in the field.
The team re-purposed, re-wired and roboticized farm equipment ranging from a Japanese tractor to a 25-year-old combine. Drones served as scouts to survey the operation and collect samples to help the team monitor the progress of the barley. At the end of the season, the robo farmers harvested about 4.5 tons of barley at a price tag of £200,000.
“This project aimed to prove that there’s no technological reason why a field can’t be farmed without humans working the land directly now, and we’ve done that,” said Martin Abell, mechatronics researcher for Precision Decisions, which partnered with Harper Adams, in a press release.
I, Robot Farmer
The Harper Adams experiment is the latest example of how machines are disrupting the agricultural industry. Around the same time that the Hands Free Hectare combine was harvesting barley, Deere & Company announced it would acquire a startup called Blue River Technology for a reported $305 million.
Blue River has developed a “see-and-spray” system that combines computer vision and artificial intelligence to discriminate between crops and weeds. It hits the former with fertilizer and blasts the latter with herbicides with such precision that it can eliminate 90 percent of the chemicals used in conventional agriculture.
It’s not just farmland that’s getting a helping hand from robots. A California company called Abundant Robotics, spun out of the nonprofit research institute SRI International, is developing robots capable of picking apples with vacuum-like arms that suck the fruit straight off the trees in the orchards.
“Traditional robots were designed to perform very specific tasks over and over again. But the robots that will be used in food and agricultural applications will have to be much more flexible than what we’ve seen in automotive manufacturing plants in order to deal with natural variation in food products or the outdoor environment,” Dan Harburg, an associate at venture capital firm Anterra Capital who previously worked at a Massachusetts-based startup making a robotic arm capable of grabbing fruit, told AgFunder News.
“This means ag-focused robotics startups have to design systems from the ground up, which can take time and money, and their robots have to be able to complete multiple tasks to avoid sitting on the shelf for a significant portion of the year,” he noted.
Eyes in the Sky
It will take more than an army of robotic tractors to grow a successful crop. The farm of the future will rely on drones, satellites, and other airborne instruments to provide data about their crops on the ground.
Companies like Descartes Labs, for instance, employ machine learning to analyze satellite imagery to forecast soy and corn yields. The Los Alamos, New Mexico startup collects five terabytes of data every day from multiple satellite constellations, including NASA and the European Space Agency. Combined with weather readings and other real-time inputs, Descartes Labs can predict cornfield yields with 99 percent accuracy. Its AI platform can even assess crop health from infrared readings.
The US agency DARPA recently granted Descartes Labs $1.5 million to monitor and analyze wheat yields in the Middle East and Africa. The idea is that accurate forecasts may help identify regions at risk of crop failure, which could lead to famine and political unrest. Another company called TellusLabs out of Somerville, Massachusetts also employs machine learning algorithms to predict corn and soy yields with similar accuracy from satellite imagery.
Farmers don’t have to reach orbit to get insights on their cropland. A startup in Oakland, Ceres Imaging, produces high-resolution imagery from multispectral cameras flown across fields aboard small planes. The snapshots capture the landscape at different wavelengths, identifying insights into problems like water stress, as well as providing estimates of chlorophyll and nitrogen levels. The geo-tagged images mean farmers can easily locate areas that need to be addressed.
Growing From the Inside
Even the best intelligence—whether from drones, satellites, or machine learning algorithms—will be challenged to predict the unpredictable issues posed by climate change. That’s one reason more and more companies are betting the farm on what’s called controlled environment agriculture. Today, that doesn’t just mean fancy greenhouses, but everything from warehouse-sized, automated vertical farms to grow rooms run by robots, located not in the emptiness of Kansas or Nebraska but smack dab in the middle of the main streets of America.
Proponents of these new concepts argue these high-tech indoor farms can produce much higher yields while drastically reducing water usage and synthetic inputs like fertilizer and herbicides.
Iron Ox, out of San Francisco, is developing one-acre urban greenhouses that will be operated by robots and reportedly capable of producing the equivalent of 30 acres of farmland. Powered by artificial intelligence, a team of three robots will run the entire operation of planting, nurturing, and harvesting the crops.
Vertical farming startup Plenty, also based in San Francisco, uses AI to automate its operations, and got a $200 million vote of confidence from the SoftBank Vision Fund earlier this year. The company claims its system uses only 1 percent of the water consumed in conventional agriculture while producing 350 times as much produce. Plenty is part of a new crop of urban-oriented farms, including Bowery Farming and AeroFarms.
“What I can envision is locating a larger scale indoor farm in the economically disadvantaged food desert, in order to stimulate a broader economic impact that could create jobs and generate income for that area,” said Dr. Gary Stutte, an expert in space agriculture and controlled environment agriculture, in an interview with AgFunder News. “The indoor agriculture model is adaptable to becoming an engine for economic growth and food security in both rural and urban food deserts.”
Still, the model is not without its own challenges and criticisms. Most of what these farms can produce falls into the “leafy greens” category and often comes with a premium price, which seems antithetical to the proposed mission of creating oases in the food deserts of cities. While water usage may be minimized, the electricity required to power the operation, especially the LEDs (which played a huge part in revolutionizing indoor agriculture), are not cheap.
Still, all of these advances, from robo farmers to automated greenhouses, may need to be part of a future where nearly 10 billion people will inhabit the planet by 2050. An oft-quoted statistic from the Food and Agriculture Organization of the United Nations says the world must boost food production by 70 percent to meet the needs of the population. Technology may not save the world, but it will help feed it.
Image Credit: Valentin Valkov / Shutterstock.com Continue reading
Posted in Human Robots
#431325 Scientists develop robot with learned ...
The two main pitfalls of robots that imitate the human body are control and cost. Researchers from the MoCoTi European project have designed a prototype of a robot that learns how to actuate its own limbs, and that can be easily duplicated. The device, consisting of a control system and a tendon-driven robotic arm, might be the first step toward low-cost humanoid robotics. Continue reading
Posted in Human Robots
#431189 Researchers Develop New Tech to Predict ...
It is one of the top 10 deadliest diseases in the United States, and it cannot be cured or prevented. But new studies are finding ways to diagnose Alzheimer’s disease in its earliest stages, while some of the latest research says technologies like artificial intelligence can detect dementia years before the first symptoms occur.
These advances, in turn, will help bolster clinical trials seeking a cure or therapies to slow or prevent the disease. Catching Alzheimer’s disease or other forms of dementia early in their progression can help ease symptoms in some cases.
“Often neurodegeneration is diagnosed late when massive brain damage has already occurred,” says professor Francis L Martin at the University of Central Lancashire in the UK, in an email to Singularity Hub. “As we know more about the molecular basis of the disease, there is the possibility of clinical interventions that might slow or halt the progress of the disease, i.e., before brain damage. Extending cognitive ability for even a number of years would have huge benefit.”
Blood Diamond
Martin is the principal investigator on a project that has developed a technique to analyze blood samples to diagnose Alzheimer’s disease and distinguish between other forms of dementia.
The researchers used sensor-based technology with a diamond core to analyze about 550 blood samples. They identified specific chemical bonds within the blood after passing light through the diamond core and recording its interaction with the sample. The results were then compared against blood samples from cases of Alzheimer’s disease and other neurodegenerative diseases, along with those from healthy individuals.
“From a small drop of blood, we derive a fingerprint spectrum. That fingerprint spectrum contains numerical data, which can be inputted into a computational algorithm we have developed,” Martin explains. “This algorithm is validated for prediction of unknown samples. From this we determine sensitivity and specificity. Although not perfect, my clinical colleagues reliably tell me our results are far better than anything else they have seen.”
Martin says the breakthrough is the result of more than 10 years developing sensor-based technologies for routine screening, monitoring, or diagnosing neurodegenerative diseases and cancers.
“My vision was to develop something low-cost that could be readily applied in a typical clinical setting to handle thousands of samples potentially per day or per week,” he says, adding that the technology also has applications in environmental science and food security.
The new test can also distinguish accurately between Alzheimer’s disease and other forms of neurodegeneration, such as Lewy body dementia, which is one of the most common causes of dementia after Alzheimer’s.
“To this point, other than at post-mortem, there has been no single approach towards classifying these pathologies,” Martin notes. “MRI scanning is often used but is labor-intensive, costly, difficult to apply to dementia patients, and not a routine point-of-care test.”
Crystal Ball
Canadian researchers at McGill University believe they can predict Alzheimer’s disease up to two years before its onset using big data and artificial intelligence. They developed an algorithm capable of recognizing the signatures of dementia using a single amyloid PET scan of the brain of patients at risk of developing the disease.
Alzheimer’s is caused by the accumulation of two proteins—amyloid beta and tau. The latest research suggests that amyloid beta leads to the buildup of tau, which is responsible for damaging nerve cells and connections between cells called synapses.
The work was recently published in the journal Neurobiology of Aging.
“Despite the availability of biomarkers capable of identifying the proteins causative of Alzheimer’s disease in living individuals, the current technologies cannot predict whether carriers of AD pathology in the brain will progress to dementia,” Sulantha Mathotaarachchi, lead author on the paper and an expert in artificial neural networks, tells Singularity Hub by email.
The algorithm, trained on a population with amnestic mild cognitive impairment observed over 24 months, proved accurate 84.5 percent of the time. Mathotaarachchi says the algorithm can be trained on different populations for different observational periods, meaning the system can grow more comprehensive with more data.
“The more biomarkers we incorporate, the more accurate the prediction could be,” Mathotaarachchi adds. “However, right now, acquiring [the] required amount of training data is the biggest challenge. … In Alzheimer’s disease, it is known that the amyloid protein deposition occurs decades before symptoms onset.”
Unfortunately, the same process occurs in normal aging as well. “The challenge is to identify the abnormal patterns of deposition that lead to the disease later on,” he says
One of the key goals of the project is to improve the research in Alzheimer’s disease by ensuring those patients with the highest probability to develop dementia are enrolled in clinical trials. That will increase the efficiency of clinical programs, according to Mathotaarachchi.
“One of the most important outcomes from our study was the pilot, online, real-time prediction tool,” he says. “This can be used as a framework for patient screening before recruiting for clinical trials. … If a disease-modifying therapy becomes available for patients, a predictive tool might have clinical applications as well, by providing to the physician information regarding clinical progression.”
Pixel by Pixel Prediction
Private industry is also working toward improving science’s predictive powers when it comes to detecting dementia early. One startup called Darmiyan out of San Francisco claims its proprietary software can pick up signals before the onset of Alzheimer’s disease by up to 15 years.
Darmiyan didn’t respond to a request for comment for this article. Venture Beat reported that the company’s MRI-analyzing software “detects cell abnormalities at a microscopic level to reveal what a standard MRI scan cannot” and that the “software measures and highlights subtle microscopic changes in the brain tissue represented in every pixel of the MRI image long before any symptoms arise.”
Darmiyan claims to have a 90 percent accuracy rate and says its software has been vetted by top academic institutions like New York University, Rockefeller University, and Stanford, according to Venture Beat. The startup is awaiting FDA approval to proceed further but is reportedly working with pharmaceutical companies like Amgen, Johnson & Johnson, and Pfizer on pilot programs.
“Our technology enables smarter drug selection in preclinical animal studies, better patient selection for clinical trials, and much better drug-effect monitoring,” Darmiyan cofounder and CEO Padideh Kamali-Zare told Venture Beat.
Conclusions
An estimated 5.5 million Americans have Alzheimer’s, and one in 10 people over age 65 have been diagnosed with the disease. By mid-century, the number of Alzheimer’s patients could rise to 16 million. Health care costs in 2017 alone are estimated to be $259 billion, and by 2050 the annual price tag could be more than $1 trillion.
In sum, it’s a disease that cripples people and the economy.
Researchers are always after more data as they look to improve outcomes, with the hope of one day developing a cure or preventing the onset of neurodegeneration altogether. If interested in seeing this medical research progress, you can help by signing up on the Brain Health Registry to improve the quality of clinical trials.
Image Credit: rudall30 / Shutterstock.com Continue reading
Posted in Human Robots