Script

Simple object segmentation with excel export

Stephane Dallongeville
Publication ID: ICY-O7W2L6
Short Description Documentation Articles on this Review this Dependencies Changelog

Short Description

Here is what this script does from an input image: - apply a gaussian filter to improve the segmentation - do KMeans threshold - extract connected component as ROI - export ROI intensities values in a excel file.

Versions

  • Version 1 • Released on: 2015-01-12 16:51:43
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    Description:

    initial version

    importClass(Packages.plugins.tprovoost.scripteditor.uitools.filedialogs.FileDialog)
importClass(Packages.icy.roi.ROIUtil)
importClass(Packages.icy.util.XLSUtil)
importClass(Packages.plugins.adufour.roi.LabelExtractor)
importClass(Packages.plugins.adufour.thresholder.KMeans)
importClass(Packages.plugins.adufour.thresholder.Thresholder)
importClass(Packages.icy.sequence.SequenceUtil)
importClass(Packages.plugins.adufour.filtering.Convolution1D)
importClass(Packages.plugins.adufour.filtering.Kernels1D)
importClass(java.lang.Double)

// get current active sequence
seq = getSequence()

// get channel of interest
ch0 = SequenceUtil.extractChannel(seq, 0)

// gaussian filter
sigma = 3
kernelX = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigma).getData()
kernelY = Kernels1D.CUSTOM_GAUSSIAN.createGaussianKernel1D(sigma).getData()
Convolution1D.convolve(ch0, kernelX, kernelY, null);

// computes the kmeans thresholds for automatic thresholding
kmeans = KMeans.computeKMeansThresholds(ch0, 2)

// performs the threshold and put the result (a sequence) inside a variable
result = Thresholder.threshold(ch0, 0, kmeans, false)

// get connected components as ROIs
rois = LabelExtractor.extractLabels(result, LabelExtractor.ExtractionType.ALL_LABELS_VS_BACKGROUND, 0)

// create excel file (ask user for output file)
workbook = XLSUtil.createWorkbook(FileDialog.open())
// create excel page
page = XLSUtil.createNewPage( workbook, "my result page")

// create table header
col = 0
for(c = 0; c < seq.getSizeC(); c++)
{
    	XLSUtil.setCellString(page, col++, 0, "min intensity ch" + c)
    	XLSUtil.setCellString(page, col++, 0, "mean intensity ch" + c)
    	XLSUtil.setCellString(page, col++, 0, "max intensity ch" + c)
}

seq.beginUpdate()

// remove all ROIS from the active sequence
seq.removeAllROI()

for(i = 0; i < rois.size(); i++)
{
	roi = rois.get(i)

	// change C position to -1 (all channel) in order to retrieve stats for all channels
	pos = roi.getPosition5D()
	pos.setC(-1)
	roi.setPosition5D(pos)
	
	// add result ROI to original sequence
  	seq.addROI(roi)

	col = 0
	for(c = 0; c < seq.getSizeC(); c++)
	{
		// compute min, mean and max intensity
	        minIntensity = ROIUtil.getMinIntensity(seq, roi, -1, -1, c)
	        meanIntensity = ROIUtil.getMeanIntensity(seq, roi, -1, -1, c)
	     	maxIntensity = ROIUtil.getMaxIntensity(seq, roi, -1, -1, c)
	 
    		XLSUtil.setCellNumber(page, col++, i+1, minIntensity)
	    	XLSUtil.setCellNumber(page, col++, i+1, meanIntensity)
	    	XLSUtil.setCellNumber(page, col++, i+1, maxIntensity)
	}
}

seq.endUpdate()

XLSUtil.saveAndClose(workbook)

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