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CLIJ 1/2/x reference in category ‘binary’

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx for processing binary images.. Read more about CLIJs release cycle

Please note: CLIJ is deprecated. Make the transition to CLIJ2.

Method is available in CLIJ (deprecated release)
Method is available in CLIJ2 (stable release)
Method is available in CLIJx (experimental release)

Categories: Binary, Filter, Graphs, Labels, Math, Matrices, Measurements, Projections, Transformations

[A],[B],[C],[D],[E],[F],[G], H,[I],[J], K,[L],[M], N,[O],[P], Q, R,[S],[T], U,[V],[W], X, Y, Z

A

automaticThreshold

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.

automaticThresholdInplace (Experimental)

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]

B

binaryAnd

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.

binaryEdgeDetection

Determines pixels/voxels which are on the surface of binary objects and sets only them to 1 in the destination image. All other pixels are set to 0.

binaryFillHoles

Fills holes (pixels with value 0 surrounded by pixels with value 1) in a binary image.

binaryFillHolesSliceBySlice (Experimental)

Fills holes (pixels with value 0 surrounded by pixels with value 1) in a binary image stack slice by slice.

binaryIntersection

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 intersection operator &. All pixel values except 0 in the input images are interpreted as 1.

binaryNot

Computes a binary image (containing pixel values 0 and 1) from an image X by negating its pixel values x using the binary NOT operator !

binaryOr

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 |.

binarySubtract

Subtracts one binary image from another.

binaryUnion

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 union operator |.

binaryXOr

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 ! implementing the XOR operator.

boundingBox

Determines the bounding box of all non-zero pixels in a binary image.

C

closingBox

Apply a binary closing to the input image by calling n dilations and n erosions subsequenntly.

closingDiamond

Apply a binary closing to the input image by calling n dilations and n erosions subsequently.

connectedComponentsLabeling

Performs connected components analysis to a binary image and generates a label map.

connectedComponentsLabelingBox

Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.

connectedComponentsLabelingDiamond

Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.

connectedComponentsLabelingInplace (Experimental)

Performs connected components analysis to a binary image and generates a label map.

D

detectMaxima2DBox

Detects local maxima in a given square/cubic neighborhood.

detectMaxima3DBox

Detects local maxima in a given square/cubic neighborhood.

detectMaximaSliceBySliceBox

Detects local maxima in a given square neighborhood of an input image stack.

detectMinima2DBox

Detects local minima in a given square/cubic neighborhood.

detectMinima3DBox

Detects local minima in a given square/cubic neighborhood.

detectMinimaSliceBySliceBox

Detects local minima in a given square neighborhood of an input image stack.

dilateBox

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateSphere

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

distanceMap

Generates a distance map from a binary image.

driftCorrectionByCentroidFixation (Experimental)

Threshold the image stack, determines the centroid of the resulting binary image and translates the image stack so that its centroid sits in a defined position.

E

erodeBox

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeSphere

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

excludeLabels

This operation removes labels from a labelmap and renumbers the remaining labels.

F

findMaxima (Experimental)

Finds and labels local maxima with neighboring maxima and background above a given tolerance threshold.

G

generateBinaryOverlapMatrix

Takes two labelmaps with n and m labels and generates a (n+1)*(m+1) matrix where all pixels are set to 0 exept those where labels overlap between the label maps.

getAutomaticThreshold

The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to determine a threshold value as similar as possible to ImageJ ‘Apply Threshold’ method.

getBoundingBox

Determines the bounding box of all non-zero pixels in a binary image.

getJaccardIndex

Determines the overlap of two binary images using the Jaccard index.

getSorensenDiceCoefficient

Determines the overlap of two binary images using the Sorensen-Dice coefficent.

greyLevelAtttributeFiltering (Experimental)

Inspired by Grayscale attribute filtering from MorpholibJ library by David Legland & Ignacio Arganda-Carreras. This plugin will remove components in a grayscale image based on user-specified area (for 2D: pixels) or volume (3D: voxels). For each gray level specified in the number of bins, binary images will be generated, followed by exclusion of objects (labels) below a minimum pixel count. All the binary images for each gray level are combined to form the final image. The output is a grayscale image, where bright objects below pixel count are removed. It is recommended that low values be used for number of bins, especially for large 3D images, or it may take long time.

I

invert

Computes the negative value of all pixels in a given image.

J

jaccardIndex

Determines the overlap of two binary images using the Jaccard index.

L

labelSpots

Transforms a binary image with single pixles set to 1 to a labelled spots image.

labelToMask

Masks a single label in a label map.

labelVoronoiOctagon

Takes a labelled image and dilates the labels using a octagon shape until they touch.

localThreshold

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.

M

mask

Computes a masked image by applying a binary mask to an image.

maskLabel

Computes a masked image by applying a label mask to an image.

maskStackWithPlane

Computes a masked image by applying a binary 2D mask to an image stack.

maximumOfMaskedPixels

Determines the maximum intensity in an image, but only in pixels which have non-zero values in another mask image.

meanClosestSpotDistance

Determines the distance between pairs of closest spots in two binary images.

meanOfMaskedPixels

Determines the mean intensity in a masked image.

minimumOfMaskedPixels

Determines the minimum intensity in a masked image.

O

openingBox

Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.

openingDiamond

Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.

P

parametricWatershed (Experimental)

Apply a binary watershed to a binary image and introduce black pixels between objects.

pullAsROI

Pulls a binary image from the GPU memory and puts it on the currently active ImageJ window as region of interest.

pullBinary

Copies a binary image specified by its name from GPU memory back to ImageJ and shows it. This binary image will have 0 and 255 pixel intensities as needed for ImageJ to interpret it as binary.

S

seededWatershed (Experimental)

Takes a label map (seeds) and an input image with gray values to apply the watershed algorithm and split the image above a given threshold in labels.

skeletonize (Experimental)

Erodes a binary image until just its skeleton is left.

sorensenDiceCoefficient

Determines the overlap of two binary images using the Sorensen-Dice coefficent.

standardDeviationOfMaskedPixels

Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image.

statisticsOfBackgroundAndLabelledPixels

Determines bounding box, area (in pixels/voxels), min, max and mean intensity of background and labelled objects in a label map and corresponding pixels in the original image.

statisticsOfLabelledPixels

Determines bounding box, area (in pixels/voxels), min, max and mean intensity of labelled objects in a label map and corresponding pixels in the original image.

T

threshold

Computes a binary image with pixel values 0 and 1.

thresholdDefault

The automatic thresholder utilizes the Default threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdHuang

The automatic thresholder utilizes the Huang threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdIJ_IsoData

The automatic thresholder utilizes the IJ_IsoData threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdIntermodes

The automatic thresholder utilizes the Intermodes threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdIsoData

The automatic thresholder utilizes the IsoData threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdLi

The automatic thresholder utilizes the Li threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMaxEntropy

The automatic thresholder utilizes the MaxEntropy threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMean

The automatic thresholder utilizes the Mean threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMinError

The automatic thresholder utilizes the MinError threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMinimum

The automatic thresholder utilizes the Minimum threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMoments

The automatic thresholder utilizes the Moments threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdOtsu

The automatic thresholder utilizes the Otsu threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdPercentile

The automatic thresholder utilizes the Percentile threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdRenyiEntropy

The automatic thresholder utilizes the RenyiEntropy threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdShanbhag

The automatic thresholder utilizes the Shanbhag threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdTriangle

The automatic thresholder utilizes the Triangle threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdYen

The automatic thresholder utilizes the Yen threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

V

varianceOfMaskedPixels

Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image.

voronoiLabeling

Takes a binary image, labels connected components and dilates the regions using a octagon shape until they touch.

voronoiOctagon

Takes a binary image and dilates the regions using a octagon shape until they touch.

W

watershed

Apply a binary watershed to a binary image and introduces black pixels between objects.