A key component of any imaging workflow is a robust platform for image analysis. This became critical with the advent of volume EM imaging on VINSE鈥檚 Helios FIB-SEM, which can generate large volumes of high-resolution images. The advanced imaging PC in VINSE was purpose-built to support large-scale handling of image data. It is equipped with a dedicated professional-grade GPU, robust CPU, and ample memory to support demanding imaging tasks. Installed on the system, you鈥檒l find ImageJ, MATLAB, and Python, as well as the latest version of Amira.
Spencer Rothfuss, a structural biology graduate student in Dr. Qiangjun Zhou’s lab, uses cryogenic electron tomography (cryo-ET) to study neurons under lifelike conditions. They are studying the subcellular ultrastructure of the synapse to elucidate synaptic transmission and to define disease phenotypes. After reconstructing transmission electron micrographs into a 3D rendering of a cell, he imports the volumes into the Amira software on VINSE鈥檚 advanced imaging computer. Amira houses a suite of tools for analyzing and visualizing 2D and 3D images, and he uses it to label organelles and protein complexes, shedding light on how they interact in 3D. Several tools in Amira make this possible, including the 鈥淢agic Wand,鈥� which can select an organelle at once by filling all connected voxels. This also enables semi-automated tracing of the cytoskeleton by cross-correlating a cylinder with the raw data to identify fibers within the cell.
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