Modern light microscopic techniques provide extremely detailed insights into organs, but the terabytes of data they produce are usually nearly impossible to process. New software, developed by a team led by MDC scientist Dr. Stephan Preibisch and presented in Nature Methods (“BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples”), is helping researchers make sense of these reams of data.
It works almost like a magic wand. With the help of a few chemical tricks and ruses, scientists have for a few years now been able to render large structures like mouse brains and human organoids transparent. CLARITY is perhaps the most well-known of the many different sample clearing techniques, with which almost any object of study can be made nearly as transparent as water. This enables researchers to investigate cellular structures in ways they could previously only dream of.
And that’s not all. In 2015 another conjuring trick – called expansion microscopy – was presented in the journal Science. A research team at Massachusetts Institute of Technology (MIT) in Cambridge discovered that it was possible to expand ultrathin slices of mouse brains nearly five times their original volume, thereby allowing samples to be examined in even greater detail.
The software brings orders to the data chaos
“With the aid of modern light-sheet microscopes, which are now found in many labs, large samples processed by these methods can be rapidly imaged,” says Dr. Stephan Preibisch, head of the MDC research group on Microscopy, Image Analysis & Modeling of Developing Organisms. “The problem, however, is that the procedure generates such large quantities of data – several terabytes – that researchers often struggle to sift through and organize the data.”
To create order in the chaos, Preibisch and his team have now developed a software program that after complex reconstructing the data resembles somewhat Google Maps in 3D mode. “One can not only get an overview of the big picture, but can also zoom in to specifically examine individual structures at the desired resolution,” explains Preibisch, who has christened the software “BigStitcher.” Now, the computer program, which any interested scientist can use, has been presented in the scientific journal Nature Methods.
A team of twelve researchers from Berlin, Munich, the United Kingdom, and the United States were involved in the development. The paper’s two lead authors are David Hörl, from Ludwig-Maximilians-Universität München and the Berlin Institute for Medical Systems Biology (BIMSB) of the MDC, as well as Dr. Fabio Rojas Rusak from the MDC research group of Professor Mathias Treier. The researchers show in their paper that algorithms can be used to reconstruct and scale the data acquired by light-sheet microscopy in such a way that renders a supercomputer unnecessary. “Our software runs on any standard computer,” says Preibisch. “This allows the data to be easily shared across research teams.“
Image Credit: Janelia / MDC
News This Week
A potential milestone in cancer therapy
Researchers from the University of Bern, Inselspital, University Hospital Bern, and the University of Connecticut have made a significant breakthrough in the fight against cancer. They identified a previously unknown weak point of prostate [...]
Cardiovascular Crystal Ball: New Tool Predicts Future Heart Disease Risk
Faculty members at the UM School of Medicine have created a cutting-edge tool that enables the early identification and assessment of risks in vulnerable patients. Heart disease, being the leading cause of death globally, [...]
Scientists analyze a single atom with X-rays for the first time
In the most powerful X-ray facilities in the world, scientists can analyze samples so small they contain only 10,000 atoms. Smaller sizes have proved exceedingly difficult to achieve, but a multi-institutional team has scaled [...]
AI Demonstrates Superior Performance in Predicting Breast Cancer
AI algorithms outperformed traditional clinical risk models in a large-scale study, predicting five-year breast cancer risk more accurately. These models use mammograms as the single data source, offering potential advantages in individualizing patient care [...]
Stanford Medicine Reveals: Tiny DNA Circles Defying Genetic Laws Drive Cancer Formation
Tiny circles of DNA harbor cancer-associated oncogenes and immunomodulatory genes promoting cancer development. They arise during the transformation from pre-cancer to cancer, say Stanford Medicine-led team. Tiny circles of DNA that defy the accepted laws of [...]
Death to Blood Cancer Cells: New Drug Combination Could Revive the Power of Leading Treatment
Future clinical trials will be conducted to investigate whether the combination of chloroquine and venetoclax can prevent disease recurrence. Although new drugs have been developed to induce cancer cell death in individuals with acute [...]
Illuminating Science: X-Rays Visualize How One of Nature’s Strongest Bonds Breaks
Scientists have deciphered how an activated catalyst breaks down the strong carbon-hydrogen bonds in potent greenhouse gas methane, according to a study published in Science. Using advanced X-ray technology and quantum-chemical calculations, they tracked the [...]
Using magnetic nanoparticles as a rapid test for sepsis
Qun Ren, an Empa researcher, and her team are currently developing a diagnostic procedure that can rapidly detect life-threatening blood poisoning caused by staphylococcus bacteria. Staphylococcal sepsis is fatal in up to 40% of [...]
Team develops nanoparticles to deliver brain cancer treatment
University of Queensland researchers have developed a nanoparticle to take a chemotherapy drug into fast growing, aggressive brain tumors. Research team lead Dr. Taskeen Janjua from UQ's School of Pharmacy said the new silica [...]
Tumor Avatars – A New Approach to Personalized Cancer Treatment
A team from the University of Geneva (UNIGE) has devised a novel method for customizing treatments by testing them on artificial tumors. Determining the optimal treatment for colon cancer can be challenging as each [...]
STING Like a Bee: MIT’s Revolutionary Approach to Cancer Immunotherapy
A cancer vaccine combining checkpoint blockade therapy and a STING-activating drug eliminates tumors and prevents recurrence in mice. MIT researchers have engineered a therapeutic cancer vaccine that targets the STING pathway, vital for immune response [...]
AI Battles Superbugs: Helps Find New Antibiotic Drug To Combat Drug-Resistant Infections
The machine-learning algorithm identified a compound that kills Acinetobacter baumannii, a bacterium that lurks in many hospital settings. Using an artificial intelligence algorithm, researchers at MIT and McMaster University have identified a new antibiotic that can kill a [...]
Cancer and AI – Can ChatGPT Be Trusted?
A study published in the Journal of The National Cancer Institute Cancer Spectrum delved into the increasing use of chatbots and artificial intelligence (AI) in providing cancer-related information. The researchers discovered that these digital resources accurately [...]
Breathing New Life: Oxygen Therapy Improves Heart Function in Long COVID Patients
A small trial has found that hyperbaric oxygen therapy (HBOT) may help restore proper heart function in patients with post-COVID syndrome, with participants in the HBOT group experiencing a significant increase in global longitudinal [...]
Wireless Brain-Spine Interface: A Leap Towards Reversing Paralysis
Summary: In a pioneering study, researchers designed a wireless brain-spine interface enabling a paralyzed man to walk naturally again. The ‘digital bridge’ comprises two electronic implants — one on the brain and another on the [...]
New study reveals a gel that promises to wipe out brain cancer for good
An anti-cancer gel promises to wipe out glioblastoma permanently, a feat that's never been accomplished by any drug or surgery. So what makes this gel so special? Scientists at Johns Hopkins University (JHU) have [...]