Computational protocol: The histone deacetylase Hos2 forms an Hsp42-dependent cytoplasmic granule in quiescent yeast cells

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Protocol publication

[…] Unless otherwise specified, images are maximal projections of Z-stacks. However, for quantification of signal intensities, sum projections of Z-stacks were used. Intensity was measured using ImageJ (, and the background intensity was subtracted. When counting the number of protein foci, we examined at least 100 cells from three independent experiments by inspecting Z-sections of each cell and further confirmed using three-dimensional projections. To analyze and quantify the intensities and spatial distributions of GFP and mCherry signals, we used ImageJ and the three-dimensional graph function of softWoRx 3.7.1. For quantifying colocalization, we used JACoP () as a plug-in for ImageJ. Cell Counter ( was also used as a plug-in for ImageJ to count and categorize assemblies and cells. […]

Pipeline specifications

Software tools ImageJ, JACoP
Application Microscopic phenotype analysis
Organisms Saccharomyces cerevisiae
Chemicals Glucose