countNuclei: Count the number of distinct objects in an image (nuclei)
In karenkuang37/MyoManager: Visual analysis of skeletal muscle microscopy data

Description Usage Arguments Details Value References Examples

The following function uses several functions from EBImage to perform counting of cell nuclei in selected image. *Frame of only nuclei is recommended (typically frame #3), counting accuracy decreases if composite image is used.

1	countNuclei(img)

img

A single-frame grayscale Image containing ONLY nuclei signals.

When it comes to counting cellular objects (most commonly nuclei), The key steps are:

enhance image if objects have week signals or ill-defined edges (e.g. blurring turns nuclei into identifiable 'blobs')
apply a threshold to turn Greyscale image binary so every pixel is either 0 or 1
count objects in the foreground (with pixel value of 1)

Returns a numeric value of the number of nuclei counted.

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

Xiaolu Yang, Xuanjing Shen, Jianwu Long, Haipeng Chen, (2012): An Improved Median-based Otsu Image Thresholding Algorithm, AASRI Procedia,Volume 3, pp. 468-473, link https://www.sciencedirect.com/science/article/pii/S2212671612002338

# Example 1
rabbit = loadImage(system.file('extdata/Rabbit_01.tif', package='MyoManager'))
rNuc = selectFrame(rabbit, 3)
countNuclei(rNuc)
viewImage(rNuc)

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