upload 13 Multi-Dimensional Image Analysis

13_n-dimensional_image_data/code/blur_tiles.ijm

+
+
+open("C:/structure/teaching/lecture_applied_bioimage_analysis_2020/13_n-dimensional_image_data/data/grey_spirals.tif");
+
+run("CLIJ2 Macro Extensions", "cl_device=");
+Ext.CLIJ2_clear();
+
+input = getTitle();
+Ext.CLIJ2_push(input);
+
+// blur with normal Gaussian blur
+sigma = 10;
+Ext.CLIJ2_gaussianBlur2D(input, output_blurred, sigma, sigma);
+Ext.CLIJ2_pull(output_blurred);
+
+
+// blur with tiled Gaussian blur, no margin
+tile_size = 32;
+margin = 0;
+Ext.CLIJxt_gaussianBlur3D(input, output_blurred_tiles_no_margin, sigma, sigma, 0, tile_size, tile_size, 1, margin, margin, 0);
+Ext.CLIJ2_pull(output_blurred_tiles_no_margin);
+
+// blur with tiled Gaussian blur, no margin
+tile_size = 32;
+margin = 10;
+Ext.CLIJxt_gaussianBlur3D(input, output_blurred_tiles_margin, sigma, sigma, 0, tile_size, tile_size, 1, margin, margin, 0);
+Ext.CLIJ2_pull(output_blurred_tiles_margin);
+
+// blur with tiled Gaussian blur, no margin
+tile_size = 32;
+margin = 20;
+Ext.CLIJxt_gaussianBlur3D(input, output_blurred_tiles_margin, sigma, sigma, 0, tile_size, tile_size, 1, margin, margin, 0);
+Ext.CLIJ2_pull(output_blurred_tiles_margin);

13_n-dimensional_image_data/code/cca_tiles.ijm

+run("Close All");
+run("CLIJ2 Macro Extensions", "cl_device=");
+
+// first example: blobs
+run("Blobs (25K)");
+blobs = getTitle();
+Ext.CLIJ2_push(blobs);
+Ext.CLIJ2_create2D(blobs_scaled, 512, 512, 8);
+Ext.CLIJ2_scale2D(blobs, blobs_scaled, 512.0 / 256.0, 512.0 / 254.0, false);
+Ext.CLIJ2_thresholdOtsu(blobs_scaled, binary_blobs);
+Ext.CLIJ2_pull(binary_blobs);
+
+// first example: spirals
+open("C:/structure/teaching/lecture_applied_bioimage_analysis_2020/13_n-dimensional_image_data/data/binary_spirals.tif");
+binary_spiral = getTitle();
+Ext.CLIJ2_push(binary_spiral);
+
+
+// run global and tiles CCA
+connected_components_analysis(binary_blobs);
+connected_components_analysis(binary_spiral);
+
+
+
+function connected_components_analysis(input) {
+		
+	// normal Connected Components Labeling
+	Ext.CLIJ2_connectedComponentsLabelingBox(input, output_cca);
+	Ext.CLIJ2_pull(output_cca);
+	run("glasbey_on_dark");
+	setMinAndMax(0, 256);
+	
+	// tiled Connected Components Labeling, no margin
+	tile_size = 170;
+	margin = 0;
+	Ext.CLIJxt_connectedComponentsLabelingBox(input, output_cca_tiles_no_margin, tile_size, tile_size, 1, margin, margin, 0);
+	Ext.CLIJ2_pull(output_cca_tiles_no_margin);
+	run("glasbey_on_dark");
+	setMinAndMax(0, 256);
+
+	// clean up
+	Ext.CLIJ2_release(output_cca);
+	Ext.CLIJ2_release(output_cca_tiles_no_margin);
+}
\ No newline at end of file

13_n-dimensional_image_data/data/image_data_source.txt

+Daniela Vorkel, Robert Haase, Myers lab, CSBD / MPI CBG
\ No newline at end of file