Amira Software for cell biology

Images can aid in understanding cell structure and mechanisms.

As a cell biologist, you know how important it is to understand the intricate mechanisms of cell structure and function. However, analyzing data from various imaging systems and modalities that use different file formats can be a daunting task. Each experimental setup presents a unique challenge, and multi-scale dynamic processes require the tracking of objects of various sizes, from diffraction-limited particles to entire cells. With data sets containing anywhere from a few dozen to tens of thousands of objects, identifying and quantifying sub-cellular structures that support intracellular processes can seem overwhelming.

Thermo Scientific Amira Software is a powerful toolbox that enables cell biologists to visualize, process, and analyze complex biological data in 3D. With its advanced image processing, visualization, and analysis tools, Amira software can help you gain insights into the structure and function of cells and tissues that would be impossible to see with 2D images alone.

Whether you're studying cellular processes, tissue organization, or the effects of drugs on cells, Amira software can help you gain a deeper understanding of your images. With our easy-to-use interface and comprehensive tools, you can streamline your workflow and spend more time doing what you do best - advancing the field of cell biology. 

Imaging data

Processing

Visualization

Analysis

Introduction to Amira Software for cell biology

During this 20-minutes webinar, you will learn how to:

• Accelerate subcellular (membrane, organelle) detection and segmentation from Electron Microscopy (TEM) data using a range of readily available tools, including 3D Deep Learning model training.
• Analyze multichannel fluorescence endothelial cell culture data by performing fast and effective cleaning, segmentation, volume colocalization and neighbor cell proximity.
• Extract complex information in 3D such as detection, segmentation and penetration of cancer or immune cells to manage multichannel High Content Screening multi-well images of organoid models.
• Quickly convert, visualize and accurately process large (~100GB) multi-channel and time series light sheet tissue imaging data.

Helping scientists answer questions that enable breakthrough discoveries in life sciences, materials science, and industry.

Dr. Antentor Hinton Jr, has made extensive use of Amira Software as part of his lab’s work in mitochondrial research.

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.

Dr. Antentor Hinton Jr
Department of Molecular Physiology and Biophysics, Vanderbilt University

Matthia A. Karreman at EMBL and DKFZ, Heidelberg, Germany, uses Amira Software

This testimonial highlights the way Amira Software supported Matthia A. Karreman, MSc, PhD at EMBL and DKFZ, Heidelberg, Germany, in her project on multimodal correlative microscopy to efficiently target single tumor cells in vivo.

Matthia A. Karreman, MSc, PhD
EMBL and DKFZ, Heidelberg, Germany

"Amira Software helps to set up complex data processing workflows. The first aim was to enhance the contrast of viral and cellular membranes. We applied a combination of 3D non-local means filter and the Membrane Enhancement Filter implemented in Amira Software. An initial automated segmentation was achieved using the Top-hat segmentation tool. This initial segmentation was further manually refined utilizing a Wacom graphics tablet. Based on the refined membrane segmentation, a 3D surface was calculated using unconstrained smoothing, and the surface was visualized as 3D model."

By Steffen Klein (Chlanda lab, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany)

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