Computational protocol: Human amniotic fluid contaminants alter thyroid hormone signalling and early brain development in Xenopus embryos

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Protocol publication

[…] Image stacks were converted from their native 12 bit lif-format to series of 8bit-pngs using CLAHE (contrast limited adaptive histogram equalization, Zuiderfeld, 1994) for ImageJ (Rasband et al., http://rsbweb.nih.gov/ij/) as implemented in fiji (Saalfeld, http://fiji.sc/Enhance_Local_Contrast_%28CLAHE%29). The parameters for CLAHE were empirically tested and set to a block size of 127, 256 bins and a slope of 3 (default values). CLAHE enhances the contrast and intensity of weak signals significantly while not over-saturating strong signals. Images were analysed using Imaris software (Imaris software package, Bitplane AG, Zurich, Switzerland). The areas of individual neurons and oligodendrocytes were determined and used to calculate the mean size of individual cell volume. At least 3 brains from independent experiments were used for each experiment shown. […]

Pipeline specifications

Software tools ImageJ, CLAHE, Imaris
Application Microscopic phenotype analysis
Organisms Homo sapiens, Xenopus laevis, Caenorhabditis elegans, Drosophila melanogaster