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

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx for spot detection.. 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)
Method is available in clEsperanto (experimental)

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

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

B

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.

D

detectAndLabelMaxima (Experimental)

Determines maximum regions in a Gaussian blurred version of the original image.

detectLabelEdges

Takes a labelmap and returns an image where all pixels on label edges are set to 1 and all other pixels to 0.

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.

F

findAndLabelMaxima (Experimental)

Determine maxima with a given tolerance to surrounding maxima and background and label them.

findMaxima (Experimental)

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

L

labelSpots

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

M

morphoLibJExtendedMaxima (Experimental)

Apply MorpholibJ’s Extended Maxima to an image to produce an image where maxima regions are set to 255 and background to 0.

morphoLibJExtendedMinima (Experimental)

Apply MorpholibJ’s Extended Minima to an image to produce an image where minima regions are set to 255 and background to 0.

S

simpleITKCannyEdgeDetection (Experimental)

Apply SimpleITKs Canny edge detection filter to an image.

simpleITKZeroCrossingBasedEdgeDetection (Experimental)

Apply SimpleITKs ZeroCrossingBasedEdgeDetection to an image.

spotsToPointList

Transforms a spots image as resulting from maximum/minimum detection in an image where every column contains d pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.

V

voronoiOtsuLabeling (Experimental)

Applies two Gaussian blurs, spot detection, Otsu-thresholding and Voronoi-labeling. The thresholded binary image is flooded using the Voronoi approach starting from the found local maxima. Noise-removal sigma for spot detection and thresholding can be configured separately.

18 methods listed.