Computational protocol: Whole-Cell Analysis of Low-Density Lipoprotein Uptake by Macrophages Using STEM Tomography

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Protocol publication

[…] Tilt-series were aligned using ETomo from the IMOD software package (University of Colorado, USA) by cross-correlation followed by manual tracking. The LDL coated gold nanoparticles contained in the samples were used as fiducials for the alignment. The tomograms were then reconstructed using the weighted-back projection algorithm in ETomo from IMOD. The 3D models of the nanoparticles were generated with 3Dmod in IMOD. The 3Dmod slicer view was used to position the centre of each nanoparticle and to draw circles of correct diameter. Median filtering was applied to the maximal-intensity projection of a tomogram in order to erase single pixels and threshold of the intensity of the gold nanoparticles. The images were prepared for presentation with ImageJ (NIH). […]

Pipeline specifications

Software tools IMOD, ImageJ
Application Microscopic phenotype analysis
Organisms Allium cepa