High-Resolution 3D Imaging Workflow

Image processing was performed on a Windows 10-based workstation equipped with two Intel Xeon Gold 5120 CPUs, 1 TB of RAM, an NVIDIA Quadro P6000 GPU. To stitch the sub-volumes, the Fiji-based plugin BigStitcher^{30 (link)} was used. Image analysis was performed with Fiji^{31 (link)} and MATLAB (Mathworks), and 3D renderings were produced with ChimeraX or Arivis.

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Chakraborty T., Driscoll M.K., Jeffery E., Murphy M.M., Roudot P., Chang B.J., Vora S., Wong W.M., Nielson C.D., Zhang H., Zhemkov V., Hiremath C., De La Cruz E.D., Yating Y., Bezprozvanny I., Zhao H., Tomer R., Heintzmann R., Meeks J.P., Marciano D.K., Morrison S.J., Danuser G., Dean K.M, & Fiolka R. (2019). Light-Sheet Microscopy of Cleared Tissues with Isotropic, Subcellular Resolution. Nature methods, 16(11), 1109-1113.

Publication 2019

Xeon Gold 5120 CPUs Quadro P6000 GPU MATLAB

Gold

Corresponding Organization :

Other organizations : The University of Texas Southwestern Medical Center, Columbia University, Texas A&M University, Leibniz Institute of Photonic Technology

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Variable analysis

independent variables

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dependent variables

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control variables

Windows 10-based workstation
Two Intel Xeon Gold 5120 CPUs
1 TB of RAM
NVIDIA Quadro P6000 GPU

controls

No positive or negative controls were explicitly mentioned.

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