Computational protocol: A role for SOX9 in post-transcriptional processes: insights from the amphibian oocyte

Similar protocols

Protocol publication

[…] A specific algorithm for image processing was developed to quantify fluorescence density of each chromosome using the ImageJ software. Chromatin areas were first isolated on the Hoechst images using an automatic thresholding with the Otsu’s method after removing noise with a filter and background correction. The resulting region of interest (R.O.I) designated as MASK was then applied to the GFP images. Fluorescence density was quantified by measuring the average intensity of the GFP images inside masks previously built (Fig. ). Colocalization analyses were carried out using the ImageJ plugin “Coloc2”. […]

Pipeline specifications

Software tools ImageJ, Coloc
Application Microscopic phenotype analysis
Organisms Homo sapiens, Xenopus laevis, Xenopus tropicalis