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:
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| 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:
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| 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.
Code:
The whole code is available in a ipython notebook.
Public ipython notebook on sagemathcloud:
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:
