Computes the absolute value of every individual pixel x in a given image.
f(x) = |x|
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().absolute(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Adds a scalar value s to all pixels x of a given image X.
f(x, s) = x + s
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float scalar
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
scalar = 1.0;
// Execute operation on GPU
clij.op().addImageAndScalar(src, dst, scalar);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Calculates the sum of pairs of pixels x and y of two images X and Y.
f(x, y) = x + y
Parameters: ClearCLBuffer src, ClearCLBuffer src1, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
src1 = clij.push(src1ImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().addImages(src, src1, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
src1.close();
dst.close();
addImagesWeighted( ClearCLBuffer src, ClearCLBuffer src1, ClearCLBuffer dst, Float factor, Float factor1 )
Calculates the sum of pairs of pixels x and y from images X and Y weighted with factors a and b.
f(x, y, a, b) = x * a + y * b
Parameters: ClearCLBuffer src, ClearCLBuffer src1, ClearCLBuffer dst, Float factor, Float factor1
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
src1 = clij.push(src1ImagePlus);
dst = clij.create(src);
factor = 1.0;
factor1 = 2.0;
// Execute operation on GPU
clij.op().addImagesWeighted(src, src1, dst, factor, factor1);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
src1.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, AffineTransform3D at
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
at = new AffineTransform3D();
at.translate(4, 0, 0);
// Execute operation on GPU
clij.op().affineTransform(src, dst, at);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, float[] matrix
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().affineTransform(src, dst, matrix);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
applyVectorfield( ClearCLBuffer src, ClearCLBuffer vectorX, ClearCLBuffer vectorY, ClearCLBuffer dst )
Parameters: ClearCLBuffer src, ClearCLBuffer vectorX, ClearCLBuffer vectorY, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
vectorX = clij.push(vectorXImagePlus);
vectorY = clij.push(vectorYImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().applyVectorfield(src, vectorX, vectorY, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
vectorX.close();
vectorY.close();
dst.close();
applyVectorfield( ClearCLBuffer src, ClearCLBuffer vectorX, ClearCLBuffer vectorY, ClearCLBuffer vectorZ, ClearCLBuffer dst )
Parameters: ClearCLBuffer src, ClearCLBuffer vectorX, ClearCLBuffer vectorY, ClearCLBuffer vectorZ, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
vectorX = clij.push(vectorXImagePlus);
vectorY = clij.push(vectorYImagePlus);
vectorZ = clij.push(vectorZImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().applyVectorfield(src, vectorX, vectorY, vectorZ, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
vectorX.close();
vectorY.close();
vectorZ.close();
dst.close();
Determines the maximum projection of an image along Z. Furthermore, another image is generated containing the z-index where the maximum was found (zero based).
Parameters: ClearCLBuffer src, ClearCLBuffer dst_max, ClearCLBuffer dst_arg
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst_max = clij.create(src);
dst_arg = clij.create(src);
// Execute operation on GPU
clij.op().argMaximumZProjection(src, dst_max, dst_arg);
//show result
dst_maxImagePlus = clij.pull(dst_max);
dst_maxImagePlus.show());
dst_argImagePlus = clij.pull(dst_arg);
dst_argImagePlus.show());
// cleanup memory on GPU
src.close();
dst_max.close();
dst_arg.close();
The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]
Parameters: ClearCLBuffer src, ClearCLBuffer dst, String userSelectedMethod
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().automaticThreshold(src, dst, userSelectedMethod);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
automaticThreshold( ClearCLBuffer src, ClearCLBuffer dst, String userSelectedMethod, Float minimumGreyValue, Float maximumGreyValue, Integer numberOfBins )
The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]
Parameters: ClearCLBuffer src, ClearCLBuffer dst, String userSelectedMethod, Float minimumGreyValue, Float maximumGreyValue, Integer numberOfBins
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
minimumGreyValue = 1.0;
maximumGreyValue = 2.0;
numberOfBins = 10;
// Execute operation on GPU
clij.op().automaticThreshold(src, dst, userSelectedMethod, minimumGreyValue, maximumGreyValue, numberOfBins);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary AND operator &. All pixel values except 0 in the input images are interpreted as 1.
f(x, y) = x & y
Parameters: ClearCLBuffer src1, ClearCLBuffer src2, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src1 = clij.push(src1ImagePlus);
src2 = clij.push(src2ImagePlus);
dst = clij.create(src1);
// Execute operation on GPU
clij.op().binaryAnd(src1, src2, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src1.close();
src2.close();
dst.close();
Computes a binary image (containing pixel values 0 and 1) from and image X by negating its pixel values x using the binary NOT operator ! All pixel values except 0 in the input image are interpreted as 1.
f(x) = !x
Parameters: ClearCLBuffer src1, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src1 = clij.push(src1ImagePlus);
dst = clij.create(src1);
// Execute operation on GPU
clij.op().binaryNot(src1, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src1.close();
dst.close();
Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary OR operator |. All pixel values except 0 in the input images are interpreted as 1.f(x, y) = x | y
Parameters: ClearCLBuffer src1, ClearCLBuffer src2, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src1 = clij.push(src1ImagePlus);
src2 = clij.push(src2ImagePlus);
dst = clij.create(src1);
// Execute operation on GPU
clij.op().binaryOr(src1, src2, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src1.close();
src2.close();
dst.close();
Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary operators AND &, OR | and NOT ! All pixel values except 0 in the input images are interpreted as 1.
f(x, y) = (x & !y) | (!x & y)
Parameters: ClearCLBuffer src1, ClearCLBuffer src2, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src1 = clij.push(src1ImagePlus);
src2 = clij.push(src2ImagePlus);
dst = clij.create(src1);
// Execute operation on GPU
clij.op().binaryXOr(src1, src2, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src1.close();
src2.close();
dst.close();
Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape.
The 'fast' implementation is done separable. In case a sigma equals zero, the direction is not blurred.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float blurSigmaX, Float blurSigmaY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
blurSigmaX = 1.0;
blurSigmaY = 2.0;
// Execute operation on GPU
clij.op().blur(src, dst, blurSigmaX, blurSigmaY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape.
The 'fast' implementation is done separable. In case a sigma equals zero, the direction is not blurred.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float blurSigmaX, Float blurSigmaY, Float blurSigmaZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
blurSigmaX = 1.0;
blurSigmaY = 2.0;
blurSigmaZ = 3.0;
// Execute operation on GPU
clij.op().blur(src, dst, blurSigmaX, blurSigmaY, blurSigmaZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
blurSliceBySlice( ClearCLBuffer src, ClearCLBuffer dst, int kernelSizeX, int kernelSizeY, float sigmaX, float sigmaY )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, int kernelSizeX, int kernelSizeY, float sigmaX, float sigmaY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().blurSliceBySlice(src, dst, kernelSizeX, kernelSizeY, sigmaX, sigmaY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Copies an image.
f(x) = x
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().copy(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer planeIndex
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
planeIndex = 10;
// Execute operation on GPU
clij.op().copySlice(src, dst, planeIndex);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radiusX, Integer radiusY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radiusX = 10;
radiusY = 20;
// Execute operation on GPU
clij.op().countNonZeroPixelsLocally(src, dst, radiusX, radiusY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
countNonZeroPixelsLocallySliceBySlice( ClearCLBuffer src, ClearCLBuffer dst, Integer radiusX, Integer radiusY )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radiusX, Integer radiusY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radiusX = 10;
radiusY = 20;
// Execute operation on GPU
clij.op().countNonZeroPixelsLocallySliceBySlice(src, dst, radiusX, radiusY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
countNonZeroVoxelsLocally( ClearCLBuffer src, ClearCLBuffer dst, Integer radiusX, Integer radiusY, Integer radiusZ )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radiusX, Integer radiusY, Integer radiusZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radiusX = 10;
radiusY = 20;
radiusZ = 30;
// Execute operation on GPU
clij.op().countNonZeroVoxelsLocally(src, dst, radiusX, radiusY, radiusZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer startX, Integer startY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
startX = 10;
startY = 20;
// Execute operation on GPU
clij.op().crop(src, dst, startX, startY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer startX, Integer startY, Integer startZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
startX = 10;
startY = 20;
startZ = 30;
// Execute operation on GPU
clij.op().crop(src, dst, startX, startY, startZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
crossCorrelation( ClearCLBuffer src1, ClearCLBuffer meanSrc1, ClearCLBuffer src2, ClearCLBuffer meanSrc2, ClearCLBuffer dst, int radius, int deltaPos, int dimension )
Parameters: ClearCLBuffer src1, ClearCLBuffer meanSrc1, ClearCLBuffer src2, ClearCLBuffer meanSrc2, ClearCLBuffer dst, int radius, int deltaPos, int dimension
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src1 = clij.push(src1ImagePlus);
meanSrc1 = clij.push(meanSrc1ImagePlus);
src2 = clij.push(src2ImagePlus);
meanSrc2 = clij.push(meanSrc2ImagePlus);
dst = clij.create(src1);
// Execute operation on GPU
clij.op().crossCorrelation(src1, meanSrc1, src2, meanSrc2, dst, radius, deltaPos, dimension);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src1.close();
meanSrc1.close();
src2.close();
meanSrc2.close();
dst.close();
Detects local maxima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
// Execute operation on GPU
clij.op().detectMaximaBox(src, dst, radius);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Detects local maxima in a given square neighborhood of an input image stack. The input image stack is processed slice by slice. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
// Execute operation on GPU
clij.op().detectMaximaSliceBySliceBox(src, dst, radius);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Detects local minima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
// Execute operation on GPU
clij.op().detectMinimaBox(src, dst, radius);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Detects local minima in a given square neighborhood of an input image stack. The input image stack is processed slice by slice. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
// Execute operation on GPU
clij.op().detectMinimaSliceBySliceBox(src, dst, radius);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius, Boolean detectMaxima
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
detectMaxima = true;
// Execute operation on GPU
clij.op().detectOptima(src, dst, radius, detectMaxima);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
detectOptimaSliceBySlice( ClearCLBuffer src, ClearCLBuffer dst, Integer radius, Boolean detectMaxima )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius, Boolean detectMaxima
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
detectMaxima = true;
// Execute operation on GPU
clij.op().detectOptimaSliceBySlice(src, dst, radius, detectMaxima);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.
This method is comparable to the 'Dilate' menu in ImageJ in case it is applied to a 2D image. The only difference is that the output image contains values 0 and 1 instead of 0 and 255.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().dilateBox(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().dilateSphere(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Divides two images X and Y by each other pixel wise.
f(x, y) = x / y
Parameters: ClearCLBuffer src, ClearCLBuffer src1, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
src1 = clij.push(src1ImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().divideImages(src, src1, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
src1.close();
dst.close();
Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called 'Interpolation method: none'.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float factorX, Float factorY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
factorX = 1.0;
factorY = 2.0;
// Execute operation on GPU
clij.op().downsample(src, dst, factorX, factorY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called 'Interpolation method: none'.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float factorX, Float factorY, Float factorZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
factorX = 1.0;
factorY = 2.0;
factorZ = 3.0;
// Execute operation on GPU
clij.op().downsample(src, dst, factorX, factorY, factorZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Scales an image using scaling factors 0.5 for X and Y dimensions. The Z dimension stays untouched. The median method is applied. Thus, each pixel value in the destination image equals to the median of four corresponding pixels in the source image.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().downsampleSliceBySliceHalfMedian(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.
This method is comparable to the 'Erode' menu in ImageJ in case it is applied to a 2D image. The only difference is that the output image contains values 0 and 1 instead of 0 and 255.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().erodeBox(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().erodeSphere(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
fillHistogram( ClearCLBuffer src, ClearCLBuffer dstHistogram, Float minimumGreyValue, Float maximumGreyValue )
Parameters: ClearCLBuffer src, ClearCLBuffer dstHistogram, Float minimumGreyValue, Float maximumGreyValue
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dstHistogram = clij.create(src);
minimumGreyValue = 1.0;
maximumGreyValue = 2.0;
// Execute operation on GPU
clij.op().fillHistogram(src, dstHistogram, minimumGreyValue, maximumGreyValue);
//show result
dstHistogramImagePlus = clij.pull(dstHistogram);
dstHistogramImagePlus.show());
// cleanup memory on GPU
src.close();
dstHistogram.close();
Flips an image in X and/or Y direction depending on boolean flags.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Boolean flipx, Boolean flipy
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
flipx = true;
flipy = false;
// Execute operation on GPU
clij.op().flip(src, dst, flipx, flipy);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Flips an image in X and/or Y direction depending on boolean flags.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Boolean flipx, Boolean flipy, Boolean flipz
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
flipx = true;
flipy = false;
flipz = false;
// Execute operation on GPU
clij.op().flip(src, dst, flipx, flipy, flipz);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the gradient of gray values along X. Assuming a, b and c are three adjacent pixels in X direction. In the target image will be saved as: b = c - a;
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().gradientX(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the gradient of gray values along Y. Assuming a, b and c are three adjacent pixels in Y direction. In the target image will be saved as: b = c - a;
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().gradientY(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the gradient of gray values along Z. Assuming a, b and c are three adjacent pixels in Z direction. In the target image will be saved as: b = c - a;
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().gradientZ(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Determines the histogram of a given image.
Parameters: ClearCLBuffer image, Float minGreyValue, Float maxGreyValue, Integer numberOfBins
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
image = clij.push(imageImagePlus);
minGreyValue = 1.0;
maxGreyValue = 2.0;
numberOfBins = 10;
// Execute operation on GPU
resultHistogram = clij.op().histogram(image, minGreyValue, maxGreyValue, numberOfBins);
//show result
print(resultHistogram);
// cleanup memory on GPU
image.close();
Computes the negative value of all pixels in a given image. It is recommended to convert images to 32-bit float before applying this operation.
f(x) = - x
For binary images, use binaryNot.
Parameters: ClearCLBuffer input3d, ClearCLBuffer output3d
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
input3d = clij.push(input3dImagePlus);
output3d = clij.create(input3d);
// Execute operation on GPU
clij.op().invert(input3d, output3d);
//show result
output3dImagePlus = clij.pull(output3d);
output3dImagePlus.show());
// cleanup memory on GPU
input3d.close();
output3d.close();
Computes a binary image with pixel values 0 and 1 depending on if a pixel value x in image X was above of equal to the pixel value m in mask image M.
f(x) = (1 if (x >= m)); (0 otherwise)
Parameters: ClearCLBuffer src, ClearCLBuffer dst, ClearCLBuffer threshold
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
threshold = clij.push(thresholdImagePlus);
// Execute operation on GPU
clij.op().localThreshold(src, dst, threshold);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
threshold.close();
Computes a masked image by applying a mask to an image. All pixel values x of image X will be copied to the destination image in case pixel value m at the same position in the mask image is not equal to zero.
f(x,m) = (x if (m != 0); (0 otherwise))
Parameters: ClearCLBuffer src, ClearCLBuffer mask, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
mask = clij.push(maskImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().mask(src, mask, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
mask.close();
dst.close();
Computes a masked image by applying a 2D mask to an image stack. All pixel values x of image X will be copied to the destination image in case pixel value m at the same spatial position in the mask image is not equal to zero.
f(x,m) = (x if (m != 0); (0 otherwise))
Parameters: ClearCLBuffer src, ClearCLBuffer mask, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
mask = clij.push(maskImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().maskStackWithPlane(src, mask, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
mask.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, int radiusX, int radiusY, int radiusZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().maximumBox(src, dst, radiusX, radiusY, radiusZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
// Execute operation on GPU
clij.op().maximumIJ(src, dst, radius);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the maximum of a constant scalar s and each pixel value x in a given image X.
f(x, s) = max(x, s)
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float valueB
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
valueB = 1.0;
// Execute operation on GPU
clij.op().maximumImageAndScalar(src, dst, valueB);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the maximum of a pair of pixel values x, y from two given images X and Y.
f(x, s) = max(x, y)
Parameters: ClearCLBuffer src, ClearCLBuffer src1, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
src1 = clij.push(src1ImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().maximumImages(src, src1, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
src1.close();
dst.close();
Determines the maximum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column 'Max'.
Parameters: ClearCLBuffer clImage
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
clImage = clij.push(clImageImagePlus);
// Execute operation on GPU
resultMaximumOfAllPixels = clij.op().maximumOfAllPixels(clImage);
//show result
print(resultMaximumOfAllPixels);
// cleanup memory on GPU
clImage.close();
maximumSliceBySliceSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY )
Computes the local maximum of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice. The ellipses size is specified by its half-width and half-height (radius).
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().maximumSliceBySliceSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().maximumSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
maximumSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
kernelSizeZ = 30;
// Execute operation on GPU
clij.op().maximumSphere(src, dst, kernelSizeX, kernelSizeY, kernelSizeZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
maximumXYZProjection( ClearCLBuffer src, ClearCLBuffer dst_max, Integer projectedDimensionX, Integer projectedDimensionY, Integer projectedDimension )
Determines the maximum projection of an image along a given dimension. Furthermore, the X and Y dimesions of the resulting image must be specified by the user according to its definition: X = 0 Y = 1 Z = 2
Parameters: ClearCLBuffer src, ClearCLBuffer dst_max, Integer projectedDimensionX, Integer projectedDimensionY, Integer projectedDimension
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst_max = clij.create(src);
projectedDimensionX = 10;
projectedDimensionY = 20;
projectedDimension = 30;
// Execute operation on GPU
clij.op().maximumXYZProjection(src, dst_max, projectedDimensionX, projectedDimensionY, projectedDimension);
//show result
dst_maxImagePlus = clij.pull(dst_max);
dst_maxImagePlus.show());
// cleanup memory on GPU
src.close();
dst_max.close();
Determines the maximum projection of an image along Z.
Parameters: ClearCLBuffer src, ClearCLBuffer dst_max
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst_max = clij.create(src);
// Execute operation on GPU
clij.op().maximumZProjection(src, dst_max);
//show result
dst_maxImagePlus = clij.pull(dst_max);
dst_maxImagePlus.show());
// cleanup memory on GPU
src.close();
dst_max.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, int radiusX, int radiusY, int radiusZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().meanBox(src, dst, radiusX, radiusY, radiusZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
// Execute operation on GPU
clij.op().meanIJ(src, dst, radius);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
meanSliceBySliceSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY )
Computes the local mean average of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice. The ellipses size is specified by its half-width and half-height (radius).
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().meanSliceBySliceSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().meanSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
meanSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
kernelSizeZ = 30;
// Execute operation on GPU
clij.op().meanSphere(src, dst, kernelSizeX, kernelSizeY, kernelSizeZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Determines the mean average projection of an image along Z.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().meanZProjection(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
medianSliceBySliceSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY )
Computes the local median of a pixels ellipsoidal neighborhood. This is done slice-by-slice in a 3D image stack. The ellipses size is specified by its half-width and half-height (radius).
For technical reasons, the area of the ellipse must have less than 1000 pixels.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().medianSliceBySliceSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().medianSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
medianSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
kernelSizeZ = 30;
// Execute operation on GPU
clij.op().medianSphere(src, dst, kernelSizeX, kernelSizeY, kernelSizeZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, int radiusX, int radiusY, int radiusZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().minimumBox(src, dst, radiusX, radiusY, radiusZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer radius
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
radius = 10;
// Execute operation on GPU
clij.op().minimumIJ(src, dst, radius);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the maximum of a constant scalar s and each pixel value x in a given image X.
f(x, s) = min(x, s)
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float valueB
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
valueB = 1.0;
// Execute operation on GPU
clij.op().minimumImageAndScalar(src, dst, valueB);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Computes the minimum of a pair of pixel values x, y from two given images X and Y.
f(x, s) = min(x, y)
Parameters: ClearCLBuffer src, ClearCLBuffer src1, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
src1 = clij.push(src1ImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().minimumImages(src, src1, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
src1.close();
dst.close();
Determines the minimum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column 'Min'.
Parameters: ClearCLBuffer clImage
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
clImage = clij.push(clImageImagePlus);
// Execute operation on GPU
resultMinimumOfAllPixels = clij.op().minimumOfAllPixels(clImage);
//show result
print(resultMinimumOfAllPixels);
// cleanup memory on GPU
clImage.close();
minimumSliceBySliceSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY )
Computes the local minimum of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice. The ellipses size is specified by its half-width and half-height (radius).
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().minimumSliceBySliceSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
// Execute operation on GPU
clij.op().minimumSphere(src, dst, kernelSizeX, kernelSizeY);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
minimumSphere( ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ )
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer kernelSizeX, Integer kernelSizeY, Integer kernelSizeZ
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
kernelSizeX = 10;
kernelSizeY = 20;
kernelSizeZ = 30;
// Execute operation on GPU
clij.op().minimumSphere(src, dst, kernelSizeX, kernelSizeY, kernelSizeZ);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Determines the minimum projection of an image along Z.
Parameters: ClearCLBuffer src, ClearCLBuffer dst_min
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst_min = clij.create(src);
// Execute operation on GPU
clij.op().minimumZProjection(src, dst_min);
//show result
dst_minImagePlus = clij.pull(dst_min);
dst_minImagePlus.show());
// cleanup memory on GPU
src.close();
dst_min.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Integer dimension
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
dimension = 10;
// Execute operation on GPU
clij.op().multiplyImageAndCoordinate(src, dst, dimension);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Multiplies all pixels value x in a given image X with a constant scalar s.
f(x, s) = x * s
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float scalar
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
scalar = 1.0;
// Execute operation on GPU
clij.op().multiplyImageAndScalar(src, dst, scalar);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Multiplies all pairs of pixel values x and y from two image X and Y.
f(x, y) = x * y
Parameters: ClearCLBuffer src, ClearCLBuffer src1, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
src1 = clij.push(src1ImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().multiplyImages(src, src1, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
src1.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, float[] scalars
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().multiplySliceBySliceWithScalars(src, dst, scalars);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Multiplies all pairs of pixel values x and y from an image stack X and a 2D image Y. x and y are at the same spatial position within a plane.
f(x, y) = x * y
Parameters: ClearCLBuffer input3d, ClearCLBuffer input2d, ClearCLBuffer output3d
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
input3d = clij.push(input3dImagePlus);
input2d = clij.push(input2dImagePlus);
output3d = clij.create(input3d);
// Execute operation on GPU
clij.op().multiplyStackWithPlane(input3d, input2d, output3d);
//show result
output3dImagePlus = clij.pull(output3d);
output3dImagePlus.show());
// cleanup memory on GPU
input3d.close();
input2d.close();
output3d.close();
particleImageVelocimetry2D( ClearCLBuffer input1, ClearCLBuffer input2, ClearCLBuffer vfX, ClearCLBuffer vfY, Integer maxDelta )
Parameters: ClearCLBuffer input1, ClearCLBuffer input2, ClearCLBuffer vfX, ClearCLBuffer vfY, Integer maxDelta
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
input1 = clij.push(input1ImagePlus);
input2 = clij.push(input2ImagePlus);
vfX = clij.push(vfXImagePlus);
vfY = clij.push(vfYImagePlus);
maxDelta = 10;
// Execute operation on GPU
clij.op().particleImageVelocimetry2D(input1, input2, vfX, vfY, maxDelta);
//show result
// cleanup memory on GPU
input1.close();
input2.close();
vfX.close();
vfY.close();
Computes all pixels value x to the power of a given exponent a.
f(x, a) = x * a
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float exponent
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
exponent = 1.0;
// Execute operation on GPU
clij.op().power(src, dst, exponent);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float deltaAngle
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
deltaAngle = 1.0;
// Execute operation on GPU
clij.op().radialProjection(src, dst, deltaAngle);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Flippes Y and Z axis of an image stack. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().resliceBottom(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Flippes X, Y and Z axis of an image stack. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().resliceLeft(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Flippes X, Y and Z axis of an image stack. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().resliceRight(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Flippes Y and Z axis of an image stack. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().resliceTop(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Rotates a given input image by 90 degrees counter-clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().rotateLeft(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Rotates a given input image by 90 degrees clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.
Parameters: ClearCLBuffer src, ClearCLBuffer dst
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
// Execute operation on GPU
clij.op().rotateRight(src, dst);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Sets all pixel values x of a given image X to a constant value v.
f(x) = v
Parameters: ClearCLBuffer clImage, Float value
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
clImage = clij.push(clImageImagePlus);
value = 1.0;
// Execute operation on GPU
clij.op().set(clImage, value);
//show result
// cleanup memory on GPU
clImage.close();
Parameters: ClearCLBuffer clImageIn, ClearCLBuffer... clImagesOut
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
clImageIn = clij.push(clImageInImagePlus);
clImagesOut = clij.push(clImagesOutImagePlus);
// Execute operation on GPU
clij.op().splitStack(clImageIn, clImagesOut);
//show result
// cleanup memory on GPU
clImageIn.close();
clImagesOut.close();
Parameters: ClearCLBuffer source1, ClearCLBuffer source2, ClearCLBuffer destination
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
source1 = clij.push(source1ImagePlus);
source2 = clij.push(source2ImagePlus);
destination = clij.create(source1);
// Execute operation on GPU
clij.op().subtract(source1, source2, destination);
//show result
destinationImagePlus = clij.pull(destination);
destinationImagePlus.show());
// cleanup memory on GPU
source1.close();
source2.close();
destination.close();
Subtracts one image X from another image Y pixel wise.
f(x, y) = x - y
Parameters: ClearCLBuffer subtrahend, ClearCLBuffer minuend, ClearCLBuffer destination
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
subtrahend = clij.push(subtrahendImagePlus);
minuend = clij.push(minuendImagePlus);
destination = clij.create(subtrahend);
// Execute operation on GPU
clij.op().subtractImages(subtrahend, minuend, destination);
//show result
destinationImagePlus = clij.pull(destination);
destinationImagePlus.show());
// cleanup memory on GPU
subtrahend.close();
minuend.close();
destination.close();
Parameters: ClearCLBuffer clImage
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
clImage = clij.push(clImageImagePlus);
// Execute operation on GPU
resultSumPixels = clij.op().sumPixels(clImage);
//show result
print(resultSumPixels);
// cleanup memory on GPU
clImage.close();
Parameters: ClearCLBuffer input
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
input = clij.push(inputImagePlus);
// Execute operation on GPU
resultSumPixelsSliceBySlice = clij.op().sumPixelsSliceBySlice(input);
//show result
print(resultSumPixelsSliceBySlice);
// cleanup memory on GPU
input.close();
Determines the sum projection of an image along Z.
Parameters: ClearCLBuffer clImage, ClearCLBuffer clReducedImage
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
clImage = clij.push(clImageImagePlus);
clReducedImage = clij.push(clReducedImageImagePlus);
// Execute operation on GPU
clij.op().sumZProjection(clImage, clReducedImage);
//show result
// cleanup memory on GPU
clImage.close();
clReducedImage.close();
Computes a binary image with pixel values 0 and 1. All pixel values x of a given input image with value larger or equal to a given threshold t will be set to 1.
f(x,t) = (1 if (x >= t); (0 otherwise))
This plugin is comparable to setting a raw threshold in ImageJ and using the 'Convert to Mask' menu.
Parameters: ClearCLBuffer src, ClearCLBuffer dst, Float threshold
Groovy example:
// init CLIJ and GPU
import net.haesleinhuepf.clij.CLIJ;
clij = CLIJ.getInstance();
// get input parameters
src = clij.push(srcImagePlus);
dst = clij.create(src);
threshold = 1.0;
// Execute operation on GPU
clij.op().threshold(src, dst, threshold);
//show result
dstImagePlus = clij.pull(dst);
dstImagePlus.show());
// cleanup memory on GPU
src.close();
dst.close();
Documented 101 methods.