Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New software designed for rapid, automated identification of dendritic spines

06.07.2018

Researchers at the Max Planck Institute for Neuroscience release open source software, connecting and building the neuroscience coding community

Is it possible for microscopes to learn a bit about the brain? Even be taught by neuroscientists to reliably recognize parts of brain cells... all on their own? Though it may seem like something straight out of "The Jetsons", a neuroscientist and software engineer in the lab of MPFI's Scientific Director, Dr. Ryohei Yasuda, Ph.D., is developing new software with the goal of vastly improving the daily life of a microscope user.


Once an image is loaded (A), pixels are converted to grayscale floating-point numbers ranging between 0 to 1. Highest probability background is identified using Otsu's method of globally thresholding. The resulting binary image (B) includes only regions of neuronal tissue. The location of each feature vector, as well as the individual values of perimeter distance features, were quantified based on a geodesic distance transform of the binary image of the dendrite (C), using the dendrite backbone as a seed location. Identification of potential spine locations by local maxima along perimeter (D).

Credit: Max Planck Florida Institute for Neuroscience

Combining a specialized algorithm, aptly named a neural network with a small amount of training, microscopes can now autonomously and efficiently identify small neuronal compartments called dendritic spines with over 90% accuracy. Just like Rosie the robotic maid, microscopes equipped with this Spine Identification software are helping scientists streamline their daily routine, bringing research one step into the future.

In recent years, there has been a rapid expansion and advancement in powerful imaging technologies, capable of taking a look inside the brain with unprecedented resolution and sensitivity. From imaging technology alone, neuroscientists have gained an immense wealth of new information about the brain. But despite many advances in implementation and capabilities, powerful microscopes (and the software running them) are still lacking when it comes to ease of use and overall user experience.

In a new study published in PLOS ONE, Dr. Michael Smirnov, Ph.D., has created an imaging software he hopes will craft a new type of experience for users.

Smirnov explains that "When engineers and scientists design cutting-edge microscopes, they usually focus on the actual physical components and design. They are mostly interested in what these imaging technologies can do, what boundaries they can break and how they perform. Far less attention is placed on how these complex technologies can be made accessible for the average user and really improve their workflow. Each time I write my software, I always think about the user first; how can I make a difference for the person using it, make their research a little easier."

The Yasuda lab studies the complex process called synaptic plasticity, which is thought to be the cellular basis of learning and memory. When single dendritic spines are stimulated, hundreds of signaling molecules are mobilized to carry new information throughout the neuron. Members of the lab investigate this process in detail utilizing 2-photon microscopy, hoping to glean insights into how the interplay of these molecules translates into memory.

Live 2-photon imaging experiments can be an intensive endeavor. Scientists must patiently sift through a neuron's dendritic arbor, scanning hundreds of spines for suitable candidates to image. Experiments are frequently repeated to amass sufficient data and those that fail mid-way must be restarted. This often unspoken aspect can quickly turn prolonged imaging into a tedious and time consuming chore, ultimately slowing scientific progress.

Dr. Smirnov's software aims to rescue neuroscientists from the humdrum of spine imaging. Weaving in an element of machine learning, the algorithm can be taught how to differentiate between dendrite backbone and dendritic spines after being fed a training data set of previously identified spines.

Once the training period finishes, the software is capable of automatedly scanning through an image and demarcating spines it comes across with high precision. Unlike previously developed programs which can be computing intensive or optimized only for post imaging analysis, Smirnov's software is fast, scalable and compatible with most live imaging setups and post analysis applications.

"We incorporated a machine learning approach, because we wanted our software to be flexible, adaptable and as easy to use as possible." Says Smirnov "The program only requires the user to input an image and specify the scale. After that, the program does the rest."

Smirnov describes that by automating the process of spine identification, the software has the potential to dramatically increase experiment workflow, shaving off hours of time. In addition, he has also made his program's code readily available to the broader neuroscience community. A move he hopes will engage the community of coders working in the field and give them the ability to freely improve upon and customize the software, making it useful for wider applications.

Dr. Smirnov notes that Scientists at MPFI are not only committed to conducting high caliber basic neuroscience research, but also look for ways to continuously improve the research process; fast tracking new discoveries and positively impacting scientists' daily lives.

Helena Decker | EurekAlert!
Further information:
http://www.maxplanckflorida.org/news-and-media/news/new-software-designed-for-rapid-automated-identification-of-dendritic-spines/
http://dx.doi.org/10.1371/journal.pone.0199589

More articles from Information Technology:

nachricht Touchscreens go 3D with buttons that pulsate and vibrate under your fingertips
14.03.2019 | Universität des Saarlandes

nachricht EU project CALADAN set to reduce manufacturing cost of Terabit/s capable optical transceivers
11.03.2019 | IHP - Leibniz-Institut für innovative Mikroelektronik

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Stellar cartography

The Potsdam Echelle Polarimetric and Spectroscopic Instrument (PEPSI) at the Large Binocular Telescope (LBT) in Arizona released its first image of the surface magnetic field of another star. In a paper in the European journal Astronomy & Astrophysics, the PEPSI team presents a Zeeman- Doppler-Image of the surface of the magnetically active star II Pegasi.

A special technique allows astronomers to resolve the surfaces of faraway stars. Those are otherwise only seen as point sources, even in the largest telescopes...

Im Focus: Heading towards a tsunami of light

Researchers at Chalmers University of Technology and the University of Gothenburg, Sweden, have proposed a way to create a completely new source of radiation. Ultra-intense light pulses consist of the motion of a single wave and can be described as a tsunami of light. The strong wave can be used to study interactions between matter and light in a unique way. Their research is now published in the scientific journal Physical Review Letters.

"This source of radiation lets us look at reality through a new angle - it is like twisting a mirror and discovering something completely different," says...

Im Focus: Revealing the secret of the vacuum for the first time

New research group at the University of Jena combines theory and experiment to demonstrate for the first time certain physical processes in a quantum vacuum

For most people, a vacuum is an empty space. Quantum physics, on the other hand, assumes that even in this lowest-energy state, particles and antiparticles...

Im Focus: Sussex scientists one step closer to a clock that could replace GPS and Galileo

Physicists in the EPic Lab at University of Sussex make crucial development in global race to develop a portable atomic clock

Scientists in the Emergent Photonics Lab (EPic Lab) at the University of Sussex have made a breakthrough to a crucial element of an atomic clock - devices...

Im Focus: Sensing shakes

A new way to sense earthquakes could help improve early warning systems

Every year earthquakes worldwide claim hundreds or even thousands of lives. Forewarning allows people to head for safety and a matter of seconds could spell...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

International Modelica Conference with 330 visitors from 21 countries at OTH Regensburg

11.03.2019 | Event News

Selection Completed: 580 Young Scientists from 88 Countries at the Lindau Nobel Laureate Meeting

01.03.2019 | Event News

LightMAT 2019 – 3rd International Conference on Light Materials – Science and Technology

28.02.2019 | Event News

 
Latest News

Levitating objects with light

19.03.2019 | Physics and Astronomy

New technique for in-cell distance determination

19.03.2019 | Life Sciences

Stellar cartography

19.03.2019 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>