getFeatureData: Generate a data frame of nuclei shape and size features
In karenkuang37/MyoManager: Visual analysis of skeletal muscle microscopy data

Description Usage Arguments Details Value References Examples

The following function uses computeFunction and computeFunction.shape from EBImage tp produce a data frame containing the following features: area, perimeter, mean radius, and eccentricity. ( elliptical eccentricity defined by sqrt(1-minoraxis^2/majoraxis^2). This value approaches 0 for rounder objects and 1 for elongated objects.

1	getFeatureData(img)

img

A single-frame grayscale Image containing ONLY the nuclei.

*Note Frame of only nuclei (typically frame #3 of composite image) is needed, since feature data extraction can only be performed on single-frame Grayscale images with defined binary objects.

Returns a data frame containing area, perimeter, mean radius, and eccentricity of each nuclei objects in the Image.

Gregoire Pau, Florian Fuchs, Oleg Sklyar, Michael Boutros, and Wolfgang Huber (2010): EBImage - an R package for image processing with applications to cellular phenotypes. Bioinformatics, 26(7), pp. 979-981, link https://bioconductor.org/packages/release/bioc/html/EBImage.html

# Example 1
rabbit = loadImage(system.file('extdata/Rabbit_02.tif', package='MyoManager'))
rNuc = selectFrame(rabbit, 3)
rNucFeatures_df = getFeatureData(rNuc)

# Example 2
mouse = loadImage(system.file('extdata/Mouse_01.tiff', package='MyoManager'))
mNuc = selectFrame(mouse, 3)
mNucFeatures_df = getFeatureData(mNuc)