labelledSpotsToPointList

Generates a coordinate list of points in a labelled spot image.

Transforms a labelmap of spots (single pixels with values 1, 2, …, n for n spots) as resulting from connected components analysis in an image where every column contains d pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.

Categories: Measurements, Labels

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clij2_-2.5.0.1.jar.

labelledSpotsToPointList often follows after

connectedComponentsLabeling (1)
labelSpots (7)

labelledSpotsToPointList is often followed by

Usage in ImageJ macro

Ext.CLIJ2_labelledSpotsToPointList(Image input_labelled_spots, Image destination_pointlist);

Usage in object oriented programming languages

Java

// init CLIJ and GPU
import net.haesleinhuepf.clij2.CLIJ2;
import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
CLIJ2 clij2 = CLIJ2.getInstance();

// get input parameters
ClearCLBuffer input_labelled_spots = clij2.push(input_labelled_spotsImagePlus);
destination_pointlist = clij2.create(input_labelled_spots);

// Execute operation on GPU
clij2.labelledSpotsToPointList(input_labelled_spots, destination_pointlist);

// show result
destination_pointlistImagePlus = clij2.pull(destination_pointlist);
destination_pointlistImagePlus.show();

// cleanup memory on GPU
clij2.release(input_labelled_spots);
clij2.release(destination_pointlist);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
input_labelled_spots = clij2.pushMat(input_labelled_spots_matrix);
destination_pointlist = clij2.create(input_labelled_spots);

% Execute operation on GPU
clij2.labelledSpotsToPointList(input_labelled_spots, destination_pointlist);

% show result
destination_pointlist = clij2.pullMat(destination_pointlist)

% cleanup memory on GPU
clij2.release(input_labelled_spots);
clij2.release(destination_pointlist);

Icy JavaScript

// init CLIJ and GPU
importClass(net.haesleinhuepf.clicy.CLICY);
importClass(Packages.icy.main.Icy);

clij2 = CLICY.getInstance();

// get input parameters
input_labelled_spots_sequence = getSequence();
input_labelled_spots = clij2.pushSequence(input_labelled_spots_sequence);
destination_pointlist = clij2.create(input_labelled_spots);

// Execute operation on GPU
clij2.labelledSpotsToPointList(input_labelled_spots, destination_pointlist);

// show result
destination_pointlist_sequence = clij2.pullSequence(destination_pointlist)
Icy.addSequence(destination_pointlist_sequence);
// cleanup memory on GPU
clij2.release(input_labelled_spots);
clij2.release(destination_pointlist);

Example notebooks

tribolium_morphometry

Example scripts

rotating_sphere.ijm
tribolium_morphometry.ijm

Back to CLIJ2 reference Back to CLIJ2 documentation

Imprint