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.

Category: Measurements

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

spotsToPointList often follows after

spotsToPointList is often followed by

Usage in ImageJ macro

Ext.CLIJ2_spotsToPointList(Image input_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_spots = clij2.push(input_spotsImagePlus);
destination_pointlist = clij2.create(input_spots);

// Execute operation on GPU
clij2.spotsToPointList(input_spots, destination_pointlist);

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

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
input_spots = clij2.pushMat(input_spots_matrix);
destination_pointlist = clij2.create(input_spots);

% Execute operation on GPU
clij2.spotsToPointList(input_spots, destination_pointlist);

% show result
destination_pointlist = clij2.pullMat(destination_pointlist)

% cleanup memory on GPU
clij2.release(input_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_spots_sequence = getSequence();
input_spots = clij2.pushSequence(input_spots_sequence);
destination_pointlist = clij2.create(input_spots);

// Execute operation on GPU
clij2.spotsToPointList(input_spots, destination_pointlist);

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

Example notebooks

spots_pointlists_matrices_tables

Example scripts

meshTouchingNeighbors.ijm
mesh_closest_points.ijm
spots_pointlists_matrices_tables.ijm
spot_distance_measurement.ijm
mesh_close_points.m
mesh_closest_points.py

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