Thursday, March 20, 2014

Combining five images into one rgb MFISH image using scikit-image implementation of HSV color space.

MFISH is a molecular cytogenetic technics using combination of fluorescent DNA probes used to recognize chromosomes and to detect some type of rearrangements.
In a previous post, five images corresponding to different fluorochromes were combined using matrix multiplication. The matrix coefficients were chosen empiracally and validated a-posteriori by the aspect of the rgb image produced.
Scikit-image is a python library implementing color space conversions for example between RGB and HSV. To display simultaneously the images of the five spectral components, or the five fluorochromes:

Five greyscaled images of the spectral components shown in false colors (cy55, cy5, SpGreen, SpOrange, TexasRed)
 The five greyscales images were first converted into 8bits rgb colors and their hue were modified with colors chosen prior combining them:
Greyscaled images converted into rgb images
Then the five images were added to produce one rgb MFISH image of type float64:

Let' produce the HSV histograms of the image:
Since the produced image lacks some contrast, the image exposition can be corrected such that the image background becomes black and the colors become brighter:

Now the histograms of the HSV chanels look like:
The linear stretch was also chosen based on the resulting rgb image.


The whole code is available in a ipython notebook.

Code on SageMathCloud:

The ipython notebook can be run on SageMathCloud. For some reasons, it's not possible to download images from github to sagemathcloud, so local images are used.

Public ipython notebook on sagemathcloud:

Images database: 

Many thanks to Tony S Yu for his help