skimage2.measure.manders_coloc_coeff#

skimage2.measure.manders_coloc_coeff(image0, image1_mask, mask=None)[source]#

Manders’ colocalization coefficient between two image channels.

Parameters:
image0ndarray of shape (M, N)

Input image (first channel). All pixel values should be non-negative.

image1_mask(M, N) ndarray of dtype bool

Binary image giving the regions of interest in the second channel. Must have same shape as image0.

mask(M, N) ndarray of dtype bool, optional

Only image0 pixel values within mask are included in the calculation. Must have same shape as image0.

Returns:
mccfloat

Manders’ colocalization coefficient.

Notes

Manders’ colocalization coefficient (MCC) was developed in the context of confocal biological microscopy, to measure the fraction of colocalizing objects in each component of a dual-channel image. Out of the total intensity of, say, channel A, how much is found within the features (objects) of, say, channel B [1]? The measure thus ranges from 0 for no colocalization to 1 for complete colocalization.

MCC is commonly used to measure the colocalization of a particular protein in a subcelullar compartment. Typically, the mask for channel B is obtained by thresholding, to segment the features from the background. In this implementation, channel B is passed directly as a mask (image1_mask), leaving the segmentation step to the user (upstream).

The implemented equation is:

\[mcc = \frac{\sum_i A_{i,coloc}}{\sum_i A_i}\]

where

  • \(A_i\) is the value of the \(i^{th}\) pixel in image0, and

  • \(A_{i, coloc} = A_i B_i\), considering that \(B_i\) is the (True or False) value of the \(i^{th}\) pixel in image1_mask cast into int or float (1 or 0, respectively).

MCC is sensitive to noise, with diffuse signal in the first channel inflating its value. Therefore, images should be processed beforehand to remove out-of-focus and background light [2].

References

[1]

Manders, E.M.M., Verbeek, F.J. and Aten, J.A. (1993), Measurement of co-localization of objects in dual-colour confocal images. Journal of Microscopy, 169: 375-382. https://doi.org/10.1111/j.1365-2818.1993.tb03313.x https://imagej.net/media/manders.pdf

[2]

Dunn, K. W., Kamocka, M. M., & McDonald, J. H. (2011). A practical guide to evaluating colocalization in biological microscopy. American journal of physiology. Cell physiology, 300(4), C723–C742. https://doi.org/10.1152/ajpcell.00462.2010