Amira Software Supports Mitochondria Research at Vanderbilt University

Visualizing mitochondria with Amira Software

Mitochondria research has benefitted greatly from enhanced visualization. Only a few decades ago, mitochondria were generally depicted as uniform in appearance; since then, rapid developments in imaging technology have enabled clear visualization of several different mitochondrial types whose shape likely correlates to specialized functions. Analytical software, such as Thermo Scientific™ Amira™ Software, has played a crucial role in processing, visualizing, and analyzing cellular imaging data that led to these discoveries.

Dr. Antentor Hinton Jr., of the Department of Molecular Physiology and Biophysics, Vanderbilt University, has made extensive use of Amira Software as part of his lab’s work in mitochondria research. They turned specifically to Amira Software due to the accessibility and ease of use it provides. Graduate and post-doctoral researchers often have limited time to conduct their research. The less time they must spend learning the fundamentals of their tools, the more time they can spend on their research. Dr. Andrea Marshall, a staff scientist in the Hinton Lab, notes how Amira Software empowers everyone in their lab to do vital, high-quality data analysis:

“It is simple enough that we can have our undergraduate students (and sometimes even high school students) come in and we can teach them how to use the program. They can play an integral role in the science that we do.”

Mitochondria research in 3D with FIB-SEM

The Hinton Lab utilizes focused ion beam scanning electron microscopy (FIB-SEM) and serial block-face scanning electron microscopy (SBF-SEM) to go beyond traditional 2D imaging and investigate mitochondrial structure in 3D. Through sequential application of FIB or SBF milling and high-resolution SEM imaging, they can collect a stack of 2D images to be reconstructed with Amira Software into a 3D representation of the sample. Amira Software seamlessly integrates with their Thermo Scientific instruments, making this a highly intuitive process. When asked about the analytical capabilities of Amira Software, Hinton notes:

“Amira Software is crucial for visualizing SBF-SEM (serial block-face SEM) and FIB-SEM images, so we can analyze the 3D morphology of organelles. The label analysis option allows us to quantify parameters such as area, volume, perimeter, and length. Additionally, MatLab allows for other custom quantifications to be determined, such as the mitochondrial complexity index or sphericity.”

Their hope is that these volumetric observations provide a clearer understanding of structure-function relationships in mitochondria, and how they relate to disease. As Hinton describes:

“When you understand how diseases change the morphological properties of mitochondria, which are responsible for oxidative phosphorylation and implicated in many disease states, you can begin to explore methods to rescue pre-disease phenotypes and see if abnormalities in shape can be rescued.”

Simplifying training with Amira Software

Dr. Hinton has been using Amira Software for over six years, since the beginning of his postdoctoral fellowship. After initially trying other 3D reconstruction software, he found that many were not amendable for all his needs. At the recommendation of a postdoctoral mentor, he tried Amira Software. Since then, it has helped him and his group with a range of data processing tools that are not only rigorous but also easy to use, facilitating the training of new lab members. This allows them to focus more on the research rather than the intricacies of complex software. As Dr. Heather Beasley, a post-doctoral fellow in the Hinton lab, mentioned:

“If I circle the wrong mitochondria or a lipid droplet, I can actually go back and fix that, and I can visualize it every single time. That also makes it easy to train and teach students, because you can say, ‘Oh, well, actually this is what this is, let me show you how to fix it.’”

We’re excited to see the novel mitochondria research conducted by the Hinton lab and the impact this invaluable work will have on our ability to combat disease. We’re honored to have Amira Software play a critical role in their research and will continue to improve and optimize its capabilities in support of approachable and reliable data processing and analysis.

Learn more about Amira Software at thermofisher.com/amira >>

Disclaimer: Thermo Fisher Scientific provides the following information for informational purposes only, and it does not constitute an endorsement or approval by Vanderbilt University of any of the products, services or opinions of the organizations or individuals referenced therein.

Alex Ilitchev, PhD, is a scientific editor at Thermo Fisher Scientific.

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