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
Frank Boehm contributes to ‘Modern Approaches to Augmentation of Brain Function’
Modern Approaches to Augmentation of Brain Function Available from Springer Press This book covers recent advances in neural technology that provide for enhancements for brain function. It addresses a broad range of neural phenomena [...]
COVID-19: Experimental vaccine lasts 1 month at room temperature
Although the currently available COVID-19 vaccines are highly effective, limited manufacturing capacity and the need for cold-chain storage hinder their global distribution. A recent study tested the efficacy of a new adeno-associated virus (AAV) [...]
COVID vaccines hold up against severe Delta: US data
Fully vaccinated people were 11 times less likely to die of COVID and 10 times less likely to be hospitalized compared to the unvaccinated since highly contagious Delta became the most common variant, US [...]
How much protection COVID-19 vaccines give you against the Delta variant – best available data
The highly-infectious Delta coronavirus variant has spread to at least 174 countries worldwide, from the US to Australia, causing a surge in COVID-19 cases. The variant has mutations that help it partially escape the immune response produced by [...]
Without these lipid shells, there would be no mRNA vaccines for COVID-19
Fragile mRNA molecules used in COVID-19 vaccines can’t get into cells on their own. They owe their success to lipid nanoparticles that took decades to refine. Messenger RNA (mRNA) is having a moment. This [...]
COVID-19 Has Revealed Critical Knowledge Gaps on the Transmission of Respiratory Viruses
The COVID-19 pandemic has revealed critical knowledge gaps and assumptions concerning how respiratory viruses spread between hosts. Traditionally thought to be spread mainly through large respiratory droplets produced by the coughs and sneezes of sick individuals, [...]
Beyond coronavirus: the virus discoveries transforming biology
SARS-CoV-2 is just one of nonillions of viruses on our planet, and scientists are rapidly identifying legions of new species. Mya Breitbart has hunted novel viruses in African termite mounds, Antarctic seals and water [...]
COVID Vaccines Compared
There are three COVID-19 vaccines approved for use in the U.S. The Pfizer, Moderna, and Johnson & Johnson vaccines are all highly effective in protecting you from the virus that causes COVID-19. The Pfizer [...]
Covid Long-Haulers are Fighting for their Future
Many people with long COVID feel that science is failing them. Neglecting them could make the pandemic even worse. While watching the scientific community grapple with long COVID, I have thought a lot about a [...]
Experts Identify New COVID Variation in South Africa – What’s Known So Far
As a team of South African researchers we have identified a new lineage of SARS-CoV-2, the virus causing COVID-19. A lineage represents a genetically distinct virus population with a common ancestor. This virus may be designated as a variant [...]
Biden administration prepares for ‘reasonable likelihood’ of another serious pandemic
Citing the possibility of another serious pandemic, the Biden administration on Friday laid out a plan to transform the nation’s ability to respond to major biological threats. As staggering as the COVID-19 pandemic has been, [...]
Video: How Doctors Can Predict Who Dies From COVID
How doctors can predict which patients are more likely to die of COVID Several studies have come out about the COVID prognosis. As a result, we now have a powerful way to predict [...]
New COVID-19 Mu Variant Named a “Variant of Interest”
Though Delta continues to be the dominant COVID-19 strain, the World Health Organization (WHO) now says there's a new variant to keep your eye on. The B.1.621 variant, also called Mu, has just been [...]
Coronavirus vaccines cut risk of long Covid, study finds
Being fully vaccinated against Covid-19 not only cuts the risk of catching it, but also of an infection turning into long Covid, research led by King's College London suggests. It shows that in the [...]
Moderna Creates Twice as Many Antibodies as Pfizer, Study Shows
Moderna Inc.’s Covid vaccine generated more than double the antibodies of a similar shot made by Pfizer Inc. and BioNTech SE in research directly comparing immune responses to the inoculations. A study of almost [...]
Covid variant detected in South Africa ‘most mutated variant so far’
A coronavirus variant first detected in South Africa 'could be more infectious' than other mutations and have the potential to 'evade vaccines', scientists have said. The C.1.2 strain, which is linked to 'increased transmissibility', is more mutations away from [...]
