ColorSeparate
BilateralFilter
MorphologicalBinarize
LaplacianGaussianFilter
WatershedComponents
SelectComponents
Colorize
ColorNegate
ImageData

Image Processing
Computer Vision
Life Sciences

Interactively View Fluorescent Uptake of Cells

Segment and identify cells with more than a certain fluorescent uptake

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Start with an image of stained rat brain cells:

In[1]:=

img=

;

The stained cells are visible in the blue image channel:

In[2]:=

cells=ColorSeparate[img,"Blue"]

Out[2]=

The fluorescent marker is exhibited in the green channel:

In[3]:=

fluorescent=ColorSeparate[img,"Green"]

Out[3]=

Regularize the cell image with a bilateral filter:

In[4]:=

regularized=BilateralFilter[cells,1,1/12]

Out[4]=

Extract a background mask with hysteresis thresholding:

In[5]:=

background=MorphologicalBinarize@regularized

Out[5]=

Seek a seed point for every cell by looking for maxima at a given scale

In[6]:=

With[{σ=4},seeds=backgroundMinDetect[LaplacianGaussianFilter[cells,σ{3,1}]]];

In[7]:=

HighlightImage[cells,seeds]

Out[7]=

Obtain a cell segmentation via the watershed algorithm:

In[8]:=

components=ImageData[background,"Bit"]WatershedComponents[ColorNegate[regularized],seeds];Colorize[components]

Out[8]=

Measure the amount of fluorescence in each cell segment:

In[9]:=

HistogramComponentMeasurements[{fluorescent,components},"Mean"]All,2,{0,1,0.02},

...



Out[9]=

Visualize all the cells with more than a certain fluorescent uptake:

In[10]:=

ManipulateFirst@SelectComponents[{fluorescent,components},(#Mean>σ)&],{{σ,0.33},0,0.817`},

...



Out[10]=

Related Symbols

ColorSeparate
BilateralFilter
MorphologicalBinarize
LaplacianGaussianFilter
WatershedComponents
SelectComponents
Colorize
ColorNegate
ImageData

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Interactively View Fluorescent Uptake of Cells

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