clij-advanced-filters

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CLIJx - The incubator for CLIJ2 (experimental)

View the Project on GitHub clij/clij-advanced-filters

CLIJ 1/2/x reference

This reference contains all methods currently available in CLIJ2 and CLIJx. Read more about CLIJs release cycle

Please note: CLIJ2 and CLIJx are under heavy construction. This list may change at any point.

Method is available in CLIJ (stable release)
Method is available in CLIJ2 (alpha release, read more)
Method is available in CLIJx (experimental version)

[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

absolute
addImageAndScalar
addImagesWeighted
addImages
affineTransform2D
affineTransform3D
applyVectorField2D
applyVectorField3D
applyVectorfield
applyWekaModel
argMaximumZProjection
automaticThresholdInplace
automaticThreshold
averageAngleBetweenAdjacentTriangles
averageDistanceOfNClosestPoints
averageDistanceOfTouchingNeighbors

B

binaryAnd
binaryEdgeDetection
binaryIntersection
binaryNot
binaryOr
binarySubtract
binaryUnion
binaryXOr
blur2D
blur3D
blurSliceBySlice
bottomHatBox
bottomHatSphere
boundingBox

C

centerOfMass
closeIndexGapsInLabelMap
closingBox
closingDiamond
connectedComponentsLabelingInplace
connectedComponentsLabeling
copySlice
copy
countNonZeroPixels2DSphere
countNonZeroPixelsSliceBySliceSphere
countNonZeroPixels
countNonZeroVoxels3DSphere
countTouchingNeighbors
crossCorrelation

D

deformableRegistration2D
detectLabelEdges
detectMaximaBox
detectMaximaSliceBySliceBox
detectMinimaBox
detectMinimaSliceBySliceBox
differenceOfGaussian2D
differenceOfGaussian3D
differenceOfGaussianInplace3D
dilateBoxSliceBySlice
dilateBox
dilateSphereSliceBySlice
dilateSphere
distanceMap
distanceMatrixToMesh
divideImages
downsample2D
downsample3D
downsampleSliceBySliceHalfMedian
drawBox
drawLine
drawSphere
drawTwoValueLine

E

equalConstant
equal
equalizeMeanIntensitiesOfSlices
erodeBoxSliceBySlice
erodeBox
erodeSphereSliceBySlice
erodeSphere
excludeLabelsOnEdges
excludeLabelsOnSurface
excludeLabelsSubSurface
exponential
extrema

F

flip2D
flip3D

G

gaussJordan
gaussianBlur2D
gaussianBlur3D
generateDistanceMatrix
generateTouchMatrix
getSize
gradientX
gradientY
gradientZ
greaterConstant
greaterOrEqualConstant
greaterOrEqual
greater

H

histogram

I

imageToStack
invert

J

jaccardIndex

L

labelSpots
labelToMask
labelledSpotsToPointList
laplaceBox
laplaceSphere
localExtremaBox
localID
localThreshold
logarithm

M

maskLabel
maskStackWithPlane
mask
matrixEqual
maximum2DBox
maximum2DSphere
maximum3DBox
maximum3DSphere
maximumImageAndScalar
maximumImages
maximumOctagon
maximumOfAllPixels
maximumOfMaskedPixels
maximumXProjection
maximumXYZProjection
maximumYProjection
maximumZProjectionBounded
maximumZProjection
mean2DBox
mean2DSphere
mean3DBox
mean3DSphere
meanClosestSpotDistance
meanOfAllPixels
meanOfMaskedPixels
meanOfPixelsAboveThreshold
meanSliceBySliceSphere
meanSquaredError
meanZProjectionBounded
meanZProjection
median2DBox
median2DSphere
median3DBox
median3DSphere
medianZProjection
minimum2DBox
minimum2DSphere
minimum3DBox
minimum3DSphere
minimumDistanceOfTouchingNeighbors
minimumImageAndScalar
minimumImages
minimumOctagon
minimumOfAllPixels
minimumOfMaskedPixels
minimumZProjectionBounded
minimumZProjection
multiplyImageAndCoordinate
multiplyImageAndScalar
multiplyImages
multiplyMatrix
multiplyStackWithPlane

N

notEqualConstant
notEqual

O

openingBox
openingDiamond
organiseWindows

P

particleImageVelocimetryTimelapse
particleImageVelocimetry
paste2D
paste3D
pointIndexListToMesh
powerImages
power
preloadFromDisc
presign
pullAsROI
pullLabelsToROIManager

R

replaceIntensities
replaceIntensity
resample
resliceBottom
resliceLeft
resliceRight
resliceTop
rotate2D
rotate3D
rotateClockwise
rotateCounterClockwise
rotateLeft
rotateRight

S

saveAsTIF
setColumn
setNonZeroPixelsToPixelIndex
setPlane
setRampX
setRampY
setRampZ
setRow
setWhereXequalsY
setWhereXgreaterThanY
setWhereXsmallerThanY
set
shortestDistances
showGlasbeyOnGrey
showGrey
showRGB
smallerConstant
smallerOrEqualConstant
smallerOrEqual
smaller
sobel
sorensenDiceCoefficient
spotsToPointList
stackToTiles
standardDeviationOfAllPixels
standardDeviationOfMaskedPixels
standardDeviationZProjection
statisticsOfLabelledPixels
stopWatch
subtractBackground2D
subtractBackground3D
subtractImageFromScalar
subtractImages
sumOfAllPixels
sumYProjection
sumZProjection

T

tenengradFusion
thresholdDefault
thresholdHuang
thresholdIJ_IsoData
thresholdIntermodes
thresholdIsoData
thresholdLi
thresholdMaxEntropy
thresholdMean
thresholdMinError
thresholdMinimum
thresholdMoments
thresholdOtsu
thresholdPercentile
thresholdRenyiEntropy
thresholdShanbhag
thresholdTriangle
thresholdYen
threshold
topHatBox
topHatOctagonSliceBySlice
topHatOctagon
topHatSphere
touchMatrixToMesh
trainWekaModel
translate2D
translate3D
translationRegistration
translationTimelapseRegistration
transposeXY
transposeXZ
transposeYZ

V

varianceOfAllPixels
varianceOfMaskedPixels

W

watershed
writeVTKLineListToDisc
writeValuesToPositions
writeXYZPointListToDisc