Computational protocol: Klf8 regulates left-right asymmetric patterning through modulation of Kupffer’s vesicle morphogenesis and spaw expression

Similar protocols

Protocol publication

[…] The cilia length and number were quantified using LAS AF and MetaMorph software according to the following steps: (i) merge images with LAS AF for MetaMorph analysis; (ii) “Threshold Image” was set to demarcate cilia and KV cell locations, and the image was converted to grayscale; (iii) from the Arithmetic menu, “Logical AND” was selected, and KV cilia regions were defined; (iv) “Calibrate Distances” was set to define units of length (μm); and (v) the length and number of cilia were quantified by selecting “Integrated Morphometry Analysis” in the Measure menu. The area of KV lumen was quantified using ImageJ software as follows: (i) The merged grayscale images from MetaMorph were loaded in ImageJ; (ii) “Elliptical selections” was selected to demarcate cilia area; (iii) “Set scale” was selected to define units of area (μm2); and (iv) the area was determined by selecting “Measure” in the Analyze menu.In order to evaluate the DFC number, immunofluorescence confocal images of Tg(sox17:gfp) 75% epiboly embryos were merged using ImageJ software using the following steps: (i) Images were loaded into ImageJ; (ii) “Images to stack” was selected from the “Stacks” item in the Image menu; (iii) “Stacks Focuser” was selected from the “Stacks” item in the Plugins menu. DFC number was then manually counted from images with merged GFP and nuclei. […]

Pipeline specifications

Software tools MetaMorph, ImageJ
Application Microscopic phenotype analysis
Organisms Homo sapiens, Danio rerio, Caenorhabditis elegans, Mus musculus
Diseases Genetic Diseases, Inborn