Computational protocol: Quantitative morphological analysis of 2D images of complex-shaped branching biological growth forms: the example of branching thalli of liverworts

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Protocol publication

[…] We used the raster graphics editor, GIMP 2.6.12 [] and the image processing package based on ImageJ, Fiji [], to process original color sample images. The color image is converted to 8-bit grayscale, thereafter thresholding is performed using the Ostu method to obtain a binary image. However, the given threshold value is then adjusted to obtain the best binary image closet to the original image. Therefore, different threshold values are assigned for different images. We use morphological operations to improve the quality of the image by using opening operation to remove some stray foreground pixels in the background and closing operation to fill holes in the foreground. […]

Pipeline specifications

Software tools GIMP, ImageJ
Applications Miscellaneous, Microscopic phenotype analysis
Organisms Marchantia polymorpha