Skeletonize with Igor V6

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Wed, 01/07/2015 - 02:45 am

Hello,

I need to find a way to extract the skeleton of a stack of images (tiff files with 100 layers) automaticaly (1 skeleton image for each layer of the stack).

Is there a native function or a plugin in Igor V6 to perform a skeletonization ?

Thank you in advance.

I put 2 images here, one is the original image (1 layer of a stack), the second is the skeleton of the first image (made with ImageJ manualy) Image 1 Init.jpg Image 2 skeleton.jpg
Bonjour Djebulon,

To accomplish this task you need to loop over the layers of the stack, extract an image, convert it (possibly from color) to binary and then perform thinning filter on the image. I have just make changes to the thinning filter in IP6 so before you try the code below you should download the latest (http://www.wavemetrics.net/Downloads/latest/).

Function extractSkeleton(inStack)
    Wave inStack
   
    Variable iterations,isColor=0
    if(DimSize(inStack,3)>0)
        iterations=DimSize(inStack,3)
        isColor=1
    else
        iterations=DimSize(inStack,2)
    endif
   
    Variable i
    // Create an output wave of type unsigned byte:
    Make/B/U/O/N=(DimSize(inStack,0),DimSize(inStack,1),iterations) skelWave=0
   
    if(isColor==0)
        for(i=0;i<iterations;i+=1)
            ImageTransform/P=(i) getPlane inStack
            Wave M_ImagePlane      
            // apply threshold to the grayscale image:
            ImageThreshold/Q/M=1 M_ImagePlane
            Wave M_ImageThresh
           
            // apply thinning:
            MatrixFilter /T/B=0 thin M_ImageThresh
            Wave M_MatrixFilter
            ImageTransform/P=(i) /D=M_MatrixFilter setPlane skelWave
        endfor
    else
        for(i=0;i<iterations;i+=1)
            ImageTransform/CHIX=(i) getChunk inStack
            Wave M_Chunk
            ImageTransform rgb2gray M_Chunk
            Wave M_RGB2Gray
           
            // apply threshold to the grayscale image:
            ImageThreshold/Q/M=1 M_RGB2Gray
            Wave M_ImageThresh
           
            // apply thinning:
            MatrixFilter /T/B=0 thin M_ImageThresh
            Wave M_MatrixFilter
            ImageTransform/P=(i) /D=M_MatrixFilter setPlane skelWave
        endfor
    endif
   
    // cleanup:
    KillWaves/Z M_MatrixFilter,M_ImageThresh,M_RGB2Gray,M_Chunk
End


I hope this helps,

A.G.
WaveMetrics, Inc.

January 7, 2015 at 11:54 am - Permalink

Thank you very much for your answer !

I updated my version and I will try this thinning module as soon as possible.

Thank you again

January 9, 2015 at 02:18 am - Permalink

Hello, thank you very much for the function !

I managed to build a stack of skeleton for my image.

But in the result I have more than just one contour. There are a lot of segments and dots.

Is there a way to remove these segments and dots and to keep only one contour ?

Thank you very much for your answer !! :)


The attached file is a .tiff (.jpg has been added)
Skel of image stack 50.tif_.jpg Skel of image slide001.jpg

January 15, 2015 at 08:36 am - Permalink

Djebulon wrote:

But in the result I have more than just one contour. There are a lot of segments and dots.
Is there a way to remove these segments and dots and to keep only one contour ?


The skeleton algorithm does not attempt to generate a contour. It computes a skeleton for each apparent object within the image. If your image produces fragile/discontinuous contour you can improve the results by smoothing the data before computing the skeleton and/or by removing some of the short segments using morphological operators (see ImageMorphology).

A.G.
WaveMetrics, Inc.

January 15, 2015 at 11:03 am - Permalink