{"id":1302,"date":"2023-11-09T18:46:52","date_gmt":"2023-11-09T18:46:52","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/?p=1302"},"modified":"2026-02-19T21:50:40","modified_gmt":"2026-02-19T21:50:40","slug":"mitochondria-research-cell-biology-software-amira-software","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/atomic-resolution\/mitochondria-research-cell-biology-software-amira-software\/","title":{"rendered":"Amira Software Supports Mitochondria Research at Vanderbilt University"},"content":{"rendered":"

Visualizing mitochondria with Amira Software<\/strong><\/h2>\n

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\u2122 Amira\u2122 Software<\/a>, has played a crucial role in processing, visualizing, and analyzing cellular imaging data that led to these discoveries.<\/p>\n

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\u2019s 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:<\/p>\n

\u201cIt 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.\u201d<\/em><\/p>\n

Mitochondria research in 3D with FIB-SEM<\/strong><\/h2>\n

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:<\/p>\n

\u201cAmira 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.\u201d<\/em><\/p>\n

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:<\/p>\n

\u201cWhen 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.\u201d<\/em><\/p>\n