Computational protocol: Three-Dimensional Image of Cleavage Bodies in Nuclei Is Configured Using Gas Cluster Ion Beam with Time-of-Flight Secondary Ion Mass Spectrometry

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Protocol publication

[…] Ion images exported as 8-bit grayscale tiff images from TOF-SIMS data were processed using the ImageJ program (National Institutes of Health, Bethesda, MD, USA), which is available from the NIH website (http://rsbweb.nih.gov/ij/). The 3D objects were reconstructed using V-CAT software version 1.5 (RIKEN, Japan, http://vcad-hpsv.riken.jp/jp/release_software/V-Cat/) and 3D Viewer, a default plugin of ImageJ. The ion aggregations, which we call clusters in the present study, were analyzed using 3D Object Counter, an optional plugin program for ImageJ, and areas enveloping the CN−-rich region were estimated using the Kalman Stack Filter plugin, which is also available from the NIH website. For these analyses, nonspecific small clusters (<5 voxels) were ignored. Colocalization of ion signals was analyzed using the Image Calculator function in ImageJ. […]

Pipeline specifications

Software tools ImageJ, V-Cat
Applications Miscellaneous, Microscopic phenotype analysis
Organisms Mus musculus