CLIJ2
GPU accelerated image processing for everyone
Superpixel segmentation
Authors: Robert Haase, Daniela Vorkel, April 2020
Clean up ImageJ and initialize GPU:
run("Close All");
run("CLIJ2 Macro Extensions", "cl_device=[GeForce RTX 2060 SUPER]");
Ext.CLIJ2_clear();
// time measurements
time = getTime();
Ext.CLIJ2_startTimeTracing();
Load a data set
The dataset is available online. It shows a Tribolium castaneum embryo, imaged by a custom light sheet microscope, at a wavelength of 488nm (Imaging credits: Daniela Vorkel, Myers lab, MPI CBG). The data set has been resampled to a voxel size of 1x1x1 microns. The embryo expresses nuclei-GFP. We will use the dataset to detect nuclei and to generate an estimated cell-segmentation.
In addition, we use a label map of segmented cells, which got generated using this macro.
All processing steps are performed in 3D space. For visualization purpose, we are using the maximum intensity projection in Z:
path = "C:/structure/teaching/clij2_example_data/"; // load data open(path + "lund1051_resampled.tif"); input = getTitle(); open(path + "lund1051_labelled.tif"); labels = getTitle(); // push images to GPU Ext.CLIJ2_push(input); Ext.CLIJ2_push(labels); // clean up ImageJ run("Close All");
Viewing input data
Processed 3D-data will be shown in 2D, using maximum projections in Z:
show(input, "input");
show(labels, "labels");
run("glasbey_on_dark");
Determine neighborhood relationships between segmented objects
From the label map, we derive a touch-matrix to process neighboring pixel :
Ext.CLIJ2_generateTouchMatrix(labels, touch_matrix); // visualize the touch matrix Ext.CLIJ2_pull(touch_matrix);
Measure statistics
Now, we get statistics of labelled objects, in the form of a results table. From this table, we push the column PIXEL_SIZE as image back to the GPU:
run("Clear Results");
Ext.CLIJ2_statisticsOfBackgroundAndLabelledPixels(input, labels);
Ext.CLIJ2_pushResultsTableColumn(pixel_count, "PIXEL_COUNT");
run("Clear Results");
// show the pixel count vector image
Ext.CLIJ2_pull(pixel_count);
Visualize measurements in space
Next, we color-code measurements based on the label map:
Ext.CLIJ2_replaceIntensities(labels, pixel_count, pixel_count_map); show(pixel_count_map, "pixel count map"); run("Fire");
Thresholding based on derived features
Using a pixel count threshold, we segment the image by differentiating large and small objects. Thresholded 2D binary images overlap, because we look at maximum projections of 3D binary image stacks:
pixel_count_threshold = 4000;
threshold_vector_and_visualise(pixel_count, labels, pixel_count_threshold);
// This function takes a vector, binarizes it by using a threshold and
// visualizes the results as parametric image by the given label map:
function threshold_vector_and_visualise(vector, labelmap, threshold) {
// threshold the vector in two vectors:
Ext.CLIJ2_smallerConstant(vector, small_objects, threshold);
Ext.CLIJ2_greaterOrEqualConstant(vector, large_objects, threshold);
// alternative: use binaryNot
// visualise resulting binary images
Ext.CLIJ2_replaceIntensities(labelmap, small_objects, small_objects_map);
Ext.CLIJ2_replaceIntensities(labelmap, large_objects, large_objects_map);
show(small_objects_map, "below threshold");
show(large_objects_map, "above threshold");
}
Improving segmentation by superpixel filtering
Having two regions in the dataset, we can differentiate them more clearly by filtering the pixel count factor, using corresponding neighborhood relationships:
// for all objects, determine the minimum pixel count in its local neighborhood Ext.CLIJ2_minimumOfTouchingNeighbors(pixel_count, touch_matrix, filtered_pixel_count); // create a parametric image out of the filtered vector Ext.CLIJ2_replaceIntensities(labels, filtered_pixel_count, filtered_pixel_count_map); show(filtered_pixel_count_map, "filtered pixel count map"); run("Fire");
Thresholding filtered features
To apply a threshold on a filtered vector, we reuse the macro command from above:
threshold_vector_and_visualise(filtered_pixel_count, labels, pixel_count_threshold);
Renumbering label maps
Based on thresholded features, labels can get excluded and resorted within the label map.
// threshold the feature vector Ext.CLIJ2_greaterOrEqualConstant(filtered_pixel_count, binary_vector, pixel_count_threshold); // remove all labels above the threshold from the label map Ext.CLIJ2_excludeLabels(binary_vector, labels, labels_embryo); show(labels_embryo, "labels_embryo"); run("glasbey_on_dark");
Visualization of segmented ROIs
We can also show different regions using ImageJs ROIs and Overlays:
threshold_vector_and_visualise_as_rois(filtered_pixel_count, labels, input, pixel_count_threshold);
// This function takes a vector, binarizes it by thresholding
// and visualizes the results as regions of interests:
function threshold_vector_and_visualise_as_rois(vector, labelmap, input_image, threshold) {
// threshold the vector in two vectors:
Ext.CLIJ2_smallerConstant(vector, small_objects, threshold);
Ext.CLIJ2_greaterOrEqualConstant(vector, large_objects, threshold);
// alternative: use binaryNot
show(input, "Input with rois");
// visualise resulting binary images
Ext.CLIJ2_replaceIntensities(labelmap, small_objects, small_objects_map);
Ext.CLIJ2_replaceIntensities(labelmap, large_objects, large_objects_map);
Ext.CLIJ2_maximumZProjection(small_objects_map, small_objects_map_projected);
Ext.CLIJ2_maximumZProjection(large_objects_map, large_objects_map_projected);
// pull a binary image from the GPU as ROI
Ext.CLIJ2_pullAsROI(small_objects_map_projected);
run("Enlarge...", "enlarge=-1"); // prevent overlapping outlines
Overlay.addSelection("green");
// pull a binary image from the GPU as ROI
Ext.CLIJ2_pullAsROI(large_objects_map_projected);
run("Enlarge...", "enlarge=-1"); // prevent overlapping outlines
Overlay.addSelection("magenta");
temp = getTitle();
run("Flatten");
selectWindow(temp);
close();
}
Performance evaluation
Finally, a time measurement. Note that performing this workflow in ImageJ macro markdown is slower, because intermediate results are saved to disc.
print("The whole workflow took " + (getTime() - time) + " msec");
> The whole workflow took 4390 msec
Detailed time tracing for all operations
Ext.CLIJ2_stopTimeTracing(); Ext.CLIJ2_getTimeTracing(time_traces); print(time_traces);
> > timeTracing > > MaximumZProjection > < MaximumZProjection 18.816 ms > > MaximumZProjection > < MaximumZProjection 1.7192 ms > > GenerateTouchMatrix > > Set > < Set 14.2843 ms > < GenerateTouchMatrix 17.1836 ms > > StatisticsOfBackgroundAndLabelledPixels > > MaximumOfAllPixels > > MaximumZProjection > < MaximumZProjection 1.579 ms > > MaximumYProjection > < MaximumYProjection 12.9777 ms > > MaximumXProjection > < MaximumXProjection 13.0664 ms > < MaximumOfAllPixels 28.4014 ms > > StatisticsOfLabelledPixels > > CopySlice > < CopySlice 0.8603 ms > > CopySlice > < CopySlice 0.2365 ms > > CopySlice > < CopySlice 0.7719 ms > > CopySlice > < CopySlice 0.2576 ms > > CopySlice > < CopySlice 0.7953 ms > > CopySlice > < CopySlice 0.3884 ms > > CopySlice > < CopySlice 0.7982 ms > > CopySlice > < CopySlice 0.2437 ms > > CopySlice > < CopySlice 0.7158 ms > > CopySlice > < CopySlice 0.2344 ms > > CopySlice > < CopySlice 2.9421 ms > > CopySlice > < CopySlice 0.2828 ms > > CopySlice > < CopySlice 0.6794 ms > > CopySlice > < CopySlice 0.2201 ms > > CopySlice > < CopySlice 0.6428 ms > > CopySlice > < CopySlice 0.2202 ms > > CopySlice > < CopySlice 0.6541 ms > > CopySlice > < CopySlice 0.2216 ms > > CopySlice > < CopySlice 1.3088 ms > > CopySlice > < CopySlice 0.2722 ms > > CopySlice > < CopySlice 1.0033 ms > > CopySlice > < CopySlice 0.2957 ms > > CopySlice > < CopySlice 0.721 ms > > CopySlice > < CopySlice 0.2373 ms > > CopySlice > < CopySlice 0.6134 ms > > CopySlice > < CopySlice 0.1978 ms > > CopySlice > < CopySlice 0.7361 ms > > CopySlice > < CopySlice 0.276 ms > > CopySlice > < CopySlice 0.6377 ms > > CopySlice > < CopySlice 0.1921 ms > > CopySlice > < CopySlice 0.6129 ms > > CopySlice > < CopySlice 0.1911 ms > > CopySlice > < CopySlice 0.6211 ms > > CopySlice > < CopySlice 0.1886 ms > > CopySlice > < CopySlice 0.7783 ms > > CopySlice > < CopySlice 0.2712 ms > > CopySlice > < CopySlice 0.8488 ms > > CopySlice > < CopySlice 0.5745 ms > > CopySlice > < CopySlice 1.3508 ms > > CopySlice > < CopySlice 0.2968 ms > > CopySlice > < CopySlice 0.6131 ms > > CopySlice > < CopySlice 0.1819 ms > > CopySlice > < CopySlice 0.5963 ms > > CopySlice > < CopySlice 0.1896 ms > > CopySlice > < CopySlice 0.6839 ms > > CopySlice > < CopySlice 0.1865 ms > > CopySlice > < CopySlice 0.6539 ms > > CopySlice > < CopySlice 0.2128 ms > > CopySlice > < CopySlice 0.641 ms > > CopySlice > < CopySlice 0.2093 ms > > CopySlice > < CopySlice 0.6258 ms > > CopySlice > < CopySlice 0.192 ms > > CopySlice > < CopySlice 0.6017 ms > > CopySlice > < CopySlice 0.1782 ms > > CopySlice > < CopySlice 0.6035 ms > > CopySlice > < CopySlice 0.1826 ms > > CopySlice > < CopySlice 0.657 ms > > CopySlice > < CopySlice 0.1888 ms > > CopySlice > < CopySlice 0.5751 ms > > CopySlice > < CopySlice 0.1938 ms > > CopySlice > < CopySlice 0.5794 ms > > CopySlice > < CopySlice 0.1975 ms > > CopySlice > < CopySlice 0.5485 ms > > CopySlice > < CopySlice 0.1723 ms > > CopySlice > < CopySlice 0.5923 ms > > CopySlice > < CopySlice 0.1806 ms > > CopySlice > < CopySlice 0.5451 ms > > CopySlice > < CopySlice 0.1786 ms > > CopySlice > < CopySlice 0.5188 ms > > CopySlice > < CopySlice 0.1686 ms > > CopySlice > < CopySlice 0.6287 ms > > CopySlice > < CopySlice 0.2616 ms > > CopySlice > < CopySlice 0.5532 ms > > CopySlice > < CopySlice 0.1694 ms > > CopySlice > < CopySlice 0.5619 ms > > CopySlice > < CopySlice 0.1739 ms > > CopySlice > < CopySlice 0.5289 ms > > CopySlice > < CopySlice 0.1896 ms > > CopySlice > < CopySlice 0.5329 ms > > CopySlice > < CopySlice 0.1762 ms > > CopySlice > < CopySlice 0.5341 ms > > CopySlice > < CopySlice 0.2073 ms > > CopySlice > < CopySlice 0.5467 ms > > CopySlice > < CopySlice 0.172 ms > > CopySlice > < CopySlice 0.5337 ms > > CopySlice > < CopySlice 0.2597 ms > > CopySlice > < CopySlice 0.5441 ms > > CopySlice > < CopySlice 0.2308 ms > > CopySlice > < CopySlice 0.5312 ms > > CopySlice > < CopySlice 0.1694 ms > > CopySlice > < CopySlice 0.5315 ms > > CopySlice > < CopySlice 0.1748 ms > > CopySlice > < CopySlice 0.5731 ms > > CopySlice > < CopySlice 0.2184 ms > > CopySlice > < CopySlice 0.5788 ms > > CopySlice > < CopySlice 0.1757 ms > > CopySlice > < CopySlice 0.5358 ms > > CopySlice > < CopySlice 0.1701 ms > > CopySlice > < CopySlice 0.5161 ms > > CopySlice > < CopySlice 0.1745 ms > > CopySlice > < CopySlice 0.5194 ms > > CopySlice > < CopySlice 0.2523 ms > > CopySlice > < CopySlice 0.608 ms > > CopySlice > < CopySlice 0.2144 ms > > CopySlice > < CopySlice 0.6039 ms > > CopySlice > < CopySlice 0.1792 ms > > CopySlice > < CopySlice 0.5982 ms > > CopySlice > < CopySlice 0.2295 ms > > CopySlice > < CopySlice 0.6042 ms > > CopySlice > < CopySlice 0.1866 ms > > CopySlice > < CopySlice 0.6206 ms > > CopySlice > < CopySlice 0.2897 ms > > CopySlice > < CopySlice 0.536 ms > > CopySlice > < CopySlice 0.1763 ms > > CopySlice > < CopySlice 0.5144 ms > > CopySlice > < CopySlice 0.1692 ms > > CopySlice > < CopySlice 0.5397 ms > > CopySlice > < CopySlice 0.2491 ms > > CopySlice > < CopySlice 0.5443 ms > > CopySlice > < CopySlice 0.1742 ms > > CopySlice > < CopySlice 0.5314 ms > > CopySlice > < CopySlice 0.1728 ms > > CopySlice > < CopySlice 0.6147 ms > > CopySlice > < CopySlice 0.1703 ms > > CopySlice > < CopySlice 0.5792 ms > > CopySlice > < CopySlice 0.1803 ms > > CopySlice > < CopySlice 0.544 ms > > CopySlice > < CopySlice 0.1756 ms > > CopySlice > < CopySlice 0.5463 ms > > CopySlice > < CopySlice 0.2634 ms > > CopySlice > < CopySlice 0.5304 ms > > CopySlice > < CopySlice 0.1888 ms > > CopySlice > < CopySlice 0.5068 ms > > CopySlice > < CopySlice 0.2416 ms > > CopySlice > < CopySlice 0.5065 ms > > CopySlice > < CopySlice 0.1686 ms > > CopySlice > < CopySlice 0.5122 ms > > CopySlice > < CopySlice 0.1676 ms > > CopySlice > < CopySlice 0.676 ms > > CopySlice > < CopySlice 0.1919 ms > > CopySlice > < CopySlice 0.7422 ms > > CopySlice > < CopySlice 0.2458 ms > > CopySlice > < CopySlice 0.6326 ms > > CopySlice > < CopySlice 0.2224 ms > > CopySlice > < CopySlice 0.708 ms > > CopySlice > < CopySlice 0.1975 ms > > CopySlice > < CopySlice 0.676 ms > > CopySlice > < CopySlice 0.2094 ms > > CopySlice > < CopySlice 0.6613 ms > > CopySlice > < CopySlice 0.2107 ms > > CopySlice > < CopySlice 0.7997 ms > > CopySlice > < CopySlice 0.3181 ms > > CopySlice > < CopySlice 0.5702 ms > > CopySlice > < CopySlice 0.247 ms > > CopySlice > < CopySlice 0.6833 ms > > CopySlice > < CopySlice 0.2197 ms > > CopySlice > < CopySlice 1.0132 ms > > CopySlice > < CopySlice 0.229 ms > > CopySlice > < CopySlice 0.6578 ms > > CopySlice > < CopySlice 0.2718 ms > > CopySlice > < CopySlice 0.6065 ms > > CopySlice > < CopySlice 0.1937 ms > > CopySlice > < CopySlice 0.6462 ms > > CopySlice > < CopySlice 0.2375 ms > > CopySlice > < CopySlice 0.6941 ms > > CopySlice > < CopySlice 0.211 ms > > CopySlice > < CopySlice 0.6905 ms > > CopySlice > < CopySlice 0.2225 ms > > CopySlice > < CopySlice 0.7558 ms > > CopySlice > < CopySlice 0.2119 ms > > CopySlice > < CopySlice 0.7142 ms > > CopySlice > < CopySlice 0.2191 ms > > CopySlice > < CopySlice 0.586 ms > > CopySlice > < CopySlice 0.1852 ms > > CopySlice > < CopySlice 0.5575 ms > > CopySlice > < CopySlice 0.2073 ms > > CopySlice > < CopySlice 0.6916 ms > > CopySlice > < CopySlice 0.2205 ms > > CopySlice > < CopySlice 0.5861 ms > > CopySlice > < CopySlice 0.2124 ms > > CopySlice > < CopySlice 0.6027 ms > > CopySlice > < CopySlice 0.1941 ms > > CopySlice > < CopySlice 0.623 ms > > CopySlice > < CopySlice 0.2038 ms > > CopySlice > < CopySlice 0.5897 ms > > CopySlice > < CopySlice 0.2015 ms > > CopySlice > < CopySlice 0.5743 ms > > CopySlice > < CopySlice 0.1977 ms > > CopySlice > < CopySlice 0.5627 ms > > CopySlice > < CopySlice 0.2017 ms > > CopySlice > < CopySlice 0.7999 ms > > CopySlice > < CopySlice 0.2158 ms > > CopySlice > < CopySlice 0.6257 ms > > CopySlice > < CopySlice 0.2004 ms > > CopySlice > < CopySlice 0.6216 ms > > CopySlice > < CopySlice 0.2027 ms > > CopySlice > < CopySlice 0.6893 ms > > CopySlice > < CopySlice 0.2998 ms > > CopySlice > < CopySlice 0.6689 ms > > CopySlice > < CopySlice 0.1876 ms > > CopySlice > < CopySlice 0.7651 ms > > CopySlice > < CopySlice 0.2214 ms > > CopySlice > < CopySlice 0.6186 ms > > CopySlice > < CopySlice 0.2045 ms > > CopySlice > < CopySlice 0.6882 ms > > CopySlice > < CopySlice 0.283 ms > > CopySlice > < CopySlice 0.6433 ms > > CopySlice > < CopySlice 0.1897 ms > > CopySlice > < CopySlice 0.6136 ms > > CopySlice > < CopySlice 0.1948 ms > > CopySlice > < CopySlice 0.6547 ms > > CopySlice > < CopySlice 0.2358 ms > > CopySlice > < CopySlice 0.6801 ms > > CopySlice > < CopySlice 0.21 ms > > CopySlice > < CopySlice 0.6629 ms > > CopySlice > < CopySlice 0.1833 ms > > CopySlice > < CopySlice 0.5533 ms > > CopySlice > < CopySlice 0.2708 ms > > CopySlice > < CopySlice 0.5894 ms > > CopySlice > < CopySlice 0.1909 ms > > CopySlice > < CopySlice 0.644 ms > > CopySlice > < CopySlice 0.2092 ms > > CopySlice > < CopySlice 0.6005 ms > > CopySlice > < CopySlice 0.1864 ms > > CopySlice > < CopySlice 0.5754 ms > > CopySlice > < CopySlice 0.2129 ms > > CopySlice > < CopySlice 0.6921 ms > > CopySlice > < CopySlice 0.2083 ms > > CopySlice > < CopySlice 0.6477 ms > > CopySlice > < CopySlice 0.2039 ms > > CopySlice > < CopySlice 0.6099 ms > > CopySlice > < CopySlice 0.2519 ms > > CopySlice > < CopySlice 0.6174 ms > > CopySlice > < CopySlice 0.2861 ms > > CopySlice > < CopySlice 0.64 ms > > CopySlice > < CopySlice 0.1908 ms > > CopySlice > < CopySlice 0.6472 ms > > CopySlice > < CopySlice 0.2221 ms > > CopySlice > < CopySlice 0.5765 ms > > CopySlice > < CopySlice 0.2083 ms > > CopySlice > < CopySlice 0.5938 ms > > CopySlice > < CopySlice 0.2048 ms > > CopySlice > < CopySlice 0.6331 ms > > CopySlice > < CopySlice 0.1929 ms > > CopySlice > < CopySlice 0.7537 ms > > CopySlice > < CopySlice 0.2387 ms > > CopySlice > < CopySlice 0.5745 ms > > CopySlice > < CopySlice 0.2071 ms > > CopySlice > < CopySlice 0.662 ms > > CopySlice > < CopySlice 0.2059 ms > > CopySlice > < CopySlice 0.6719 ms > > CopySlice > < CopySlice 0.193 ms > > CopySlice > < CopySlice 0.6155 ms > > CopySlice > < CopySlice 0.2084 ms > > CopySlice > < CopySlice 0.6327 ms > > CopySlice > < CopySlice 0.2049 ms > > CopySlice > < CopySlice 0.5862 ms > > CopySlice > < CopySlice 0.2089 ms > > CopySlice > < CopySlice 0.7084 ms > > CopySlice > < CopySlice 0.2105 ms > > CopySlice > < CopySlice 0.641 ms > > CopySlice > < CopySlice 0.1984 ms > > CopySlice > < CopySlice 0.58 ms > > CopySlice > < CopySlice 0.2956 ms > > CopySlice > < CopySlice 0.5702 ms > > CopySlice > < CopySlice 0.1999 ms > > CopySlice > < CopySlice 0.6299 ms > > CopySlice > < CopySlice 0.2605 ms > > CopySlice > < CopySlice 0.6895 ms > > CopySlice > < CopySlice 0.2023 ms > > CopySlice > < CopySlice 0.686 ms > > CopySlice > < CopySlice 0.2827 ms > > CopySlice > < CopySlice 0.6172 ms > > CopySlice > < CopySlice 0.2249 ms > > CopySlice > < CopySlice 0.6433 ms > > CopySlice > < CopySlice 0.2057 ms > > CopySlice > < CopySlice 0.6656 ms > > CopySlice > < CopySlice 0.1996 ms > > CopySlice > < CopySlice 0.5814 ms > > CopySlice > < CopySlice 0.1756 ms > > CopySlice > < CopySlice 0.5626 ms > > CopySlice > < CopySlice 0.2812 ms > > CopySlice > < CopySlice 0.6455 ms > > CopySlice > < CopySlice 0.205 ms > > CopySlice > < CopySlice 0.691 ms > > CopySlice > < CopySlice 0.2061 ms > > CopySlice > < CopySlice 0.5902 ms > > CopySlice > < CopySlice 0.2078 ms > > CopySlice > < CopySlice 0.6603 ms > > CopySlice > < CopySlice 0.2306 ms > > CopySlice > < CopySlice 0.6994 ms > > CopySlice > < CopySlice 0.2196 ms > > CopySlice > < CopySlice 0.654 ms > > CopySlice > < CopySlice 0.2007 ms > > CopySlice > < CopySlice 0.6354 ms > > CopySlice > < CopySlice 0.2449 ms > > CopySlice > < CopySlice 0.6691 ms > > CopySlice > < CopySlice 0.1952 ms > > CopySlice > < CopySlice 0.7035 ms > > CopySlice > < CopySlice 0.2546 ms > > CopySlice > < CopySlice 0.6484 ms > > CopySlice > < CopySlice 0.1837 ms > > CopySlice > < CopySlice 0.7479 ms > > CopySlice > < CopySlice 0.3163 ms > > CopySlice > < CopySlice 0.6387 ms > > CopySlice > < CopySlice 0.2115 ms > > CopySlice > < CopySlice 0.5947 ms > > CopySlice > < CopySlice 0.183 ms > > CopySlice > < CopySlice 0.7263 ms > > CopySlice > < CopySlice 0.2112 ms > > CopySlice > < CopySlice 0.6426 ms > > CopySlice > < CopySlice 0.2887 ms > > CopySlice > < CopySlice 0.6105 ms > > CopySlice > < CopySlice 0.2683 ms > > CopySlice > < CopySlice 0.5756 ms > > CopySlice > < CopySlice 0.2182 ms > > CopySlice > < CopySlice 0.5383 ms > > CopySlice > < CopySlice 0.1925 ms > > CopySlice > < CopySlice 0.5747 ms > > CopySlice > < CopySlice 0.2763 ms > > CopySlice > < CopySlice 0.5652 ms > > CopySlice > < CopySlice 0.1978 ms > > CopySlice > < CopySlice 0.5743 ms > > CopySlice > < CopySlice 0.291 ms > > CopySlice > < CopySlice 0.5818 ms > > CopySlice > < CopySlice 0.2094 ms > > CopySlice > < CopySlice 0.6221 ms > > CopySlice > < CopySlice 0.2164 ms > > CopySlice > < CopySlice 0.6544 ms > > CopySlice > < CopySlice 0.1894 ms > > CopySlice > < CopySlice 0.5926 ms > > CopySlice > < CopySlice 0.2154 ms > > CopySlice > < CopySlice 0.6087 ms > > CopySlice > < CopySlice 0.2306 ms > > CopySlice > < CopySlice 0.5925 ms > > CopySlice > < CopySlice 0.1748 ms > > CopySlice > < CopySlice 0.5594 ms > > CopySlice > < CopySlice 0.2772 ms > > CopySlice > < CopySlice 0.7453 ms > > CopySlice > < CopySlice 0.203 ms > > CopySlice > < CopySlice 0.6488 ms > > CopySlice > < CopySlice 0.2056 ms > > CopySlice > < CopySlice 0.5891 ms > > CopySlice > < CopySlice 0.2284 ms > > CopySlice > < CopySlice 0.5785 ms > > CopySlice > < CopySlice 0.2034 ms > > CopySlice > < CopySlice 0.5931 ms > > CopySlice > < CopySlice 0.216 ms > > CopySlice > < CopySlice 0.5965 ms > > CopySlice > < CopySlice 0.1984 ms > > CopySlice > < CopySlice 0.5897 ms > > CopySlice > < CopySlice 0.2277 ms > > CopySlice > < CopySlice 0.6092 ms > > CopySlice > < CopySlice 0.2092 ms > > CopySlice > < CopySlice 0.6332 ms > > CopySlice > < CopySlice 0.2023 ms > > CopySlice > < CopySlice 0.6279 ms > > CopySlice > < CopySlice 0.2058 ms > > CopySlice > < CopySlice 0.7962 ms > > CopySlice > < CopySlice 0.3165 ms > > CopySlice > < CopySlice 0.7155 ms > > CopySlice > < CopySlice 0.2674 ms > > CopySlice > < CopySlice 0.6912 ms > > CopySlice > < CopySlice 0.2026 ms > > CopySlice > < CopySlice 0.64 ms > > CopySlice > < CopySlice 0.1816 ms > > CopySlice > < CopySlice 0.5563 ms > > CopySlice > < CopySlice 0.2133 ms > > CopySlice > < CopySlice 0.603 ms > > CopySlice > < CopySlice 0.2055 ms > > CopySlice > < CopySlice 0.719 ms > > CopySlice > < CopySlice 0.2196 ms > > CopySlice > < CopySlice 0.6674 ms > > CopySlice > < CopySlice 0.1976 ms > > CopySlice > < CopySlice 0.6959 ms > > CopySlice > < CopySlice 0.2851 ms > > CopySlice > < CopySlice 0.5828 ms > > CopySlice > < CopySlice 0.1837 ms > > CopySlice > < CopySlice 0.6213 ms > > CopySlice > < CopySlice 0.1978 ms > > CopySlice > < CopySlice 0.5672 ms > > CopySlice > < CopySlice 0.1936 ms > > CopySlice > < CopySlice 0.5879 ms > > CopySlice > < CopySlice 0.2047 ms > > CopySlice > < CopySlice 0.8409 ms > > CopySlice > < CopySlice 0.2097 ms > > CopySlice > < CopySlice 0.6779 ms > > CopySlice > < CopySlice 0.1863 ms > > CopySlice > < CopySlice 0.5813 ms > > CopySlice > < CopySlice 0.2459 ms > > CopySlice > < CopySlice 0.5595 ms > > CopySlice > < CopySlice 0.2457 ms > > CopySlice > < CopySlice 0.57 ms > > CopySlice > < CopySlice 0.1897 ms > > CopySlice > < CopySlice 0.5794 ms > > CopySlice > < CopySlice 0.1808 ms > > CopySlice > < CopySlice 0.6775 ms > > CopySlice > < CopySlice 0.2604 ms > > CopySlice > < CopySlice 0.6173 ms > > CopySlice > < CopySlice 0.1801 ms > > CopySlice > < CopySlice 0.6411 ms > > CopySlice > < CopySlice 0.1892 ms > > CopySlice > < CopySlice 0.722 ms > > CopySlice > < CopySlice 0.2638 ms > > CopySlice > < CopySlice 0.787 ms > > CopySlice > < CopySlice 0.2578 ms > > CopySlice > < CopySlice 0.6232 ms > > CopySlice > < CopySlice 0.2075 ms > > CopySlice > < CopySlice 0.8134 ms > > CopySlice > < CopySlice 0.2543 ms > > CopySlice > < CopySlice 0.7577 ms > > CopySlice > < CopySlice 0.2675 ms > > CopySlice > < CopySlice 0.6404 ms > > CopySlice > < CopySlice 0.2678 ms > > CopySlice > < CopySlice 0.8938 ms > > CopySlice > < CopySlice 0.2599 ms > > CopySlice > < CopySlice 0.7099 ms > > CopySlice > < CopySlice 0.2662 ms > > CopySlice > < CopySlice 0.6619 ms > > CopySlice > < CopySlice 0.2367 ms > > CopySlice > < CopySlice 0.6643 ms > > CopySlice > < CopySlice 0.2325 ms > > CopySlice > < CopySlice 0.6748 ms > > CopySlice > < CopySlice 0.289 ms > > CopySlice > < CopySlice 0.6242 ms > > CopySlice > < CopySlice 0.2014 ms > < StatisticsOfLabelledPixels 1143.4018 ms > < StatisticsOfBackgroundAndLabelledPixels1176.96 ms > > PushResultsTableColumn > > Copy > < Copy 0.4698 ms > < PushResultsTableColumn 1.2462 ms > > ReplaceIntensities > < ReplaceIntensities 26.0471 ms > > MaximumZProjection > < MaximumZProjection 0.8355 ms > > SmallerConstant > < SmallerConstant 13.2893 ms > > GreaterOrEqualConstant > < GreaterOrEqualConstant 12.801 ms > > ReplaceIntensities > < ReplaceIntensities 7.8833 ms > > ReplaceIntensities > < ReplaceIntensities 8.1147 ms > > MaximumZProjection > < MaximumZProjection 0.7722 ms > > MaximumZProjection > < MaximumZProjection 0.9578 ms > > MinimumOfTouchingNeighbors > < MinimumOfTouchingNeighbors 4.2116 ms > > ReplaceIntensities > < ReplaceIntensities 8.2114 ms > > MaximumZProjection > < MaximumZProjection 0.8552 ms > > SmallerConstant > < SmallerConstant 0.2937 ms > > GreaterOrEqualConstant > < GreaterOrEqualConstant 0.228 ms > > ReplaceIntensities > < ReplaceIntensities 7.9932 ms > > ReplaceIntensities > < ReplaceIntensities 8.1928 ms > > MaximumZProjection > < MaximumZProjection 0.7955 ms > > MaximumZProjection > < MaximumZProjection 0.9131 ms > > GreaterOrEqualConstant > < GreaterOrEqualConstant 0.3734 ms > > ExcludeLabels > > ReplaceIntensities > < ReplaceIntensities 7.9824 ms > < ExcludeLabels 8.3484 ms > > MaximumZProjection > < MaximumZProjection 0.7909 ms > > SmallerConstant > < SmallerConstant 0.4226 ms > > GreaterOrEqualConstant > < GreaterOrEqualConstant 0.2078 ms > > MaximumZProjection > < MaximumZProjection 0.8014 ms > > ReplaceIntensities > < ReplaceIntensities 8.1426 ms > > ReplaceIntensities > < ReplaceIntensities 8.1331 ms > > MaximumZProjection > < MaximumZProjection 0.9057 ms > > MaximumZProjection > < MaximumZProjection 0.832 ms > > PullAsROI > < PullAsROI 33.3067 ms > > PullAsROI > < PullAsROI 29.7077 ms > < timeTracing 4392.9165 ms >
Also, let’s see how much of GPU memory got used by this workflow. At the end, cleaning up remains important.
Ext.CLIJ2_reportMemory(); // finally, clean up Ext.CLIJ2_clear();
> GPU contains 23 images. > - CLIJ2_greaterOrEqualConstant_result147[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@3050f68b] 5.9 kb > - CLIJ2_greaterOrEqualConstant_result156[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@65299655] 5.9 kb > - CLIJ2_generateTouchMatrix_result133[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@6a7866a0] 8.6 Mb > - CLIJ2_greaterOrEqualConstant_result138[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@afa8429] 5.9 kb > - lund1051_labelled.tif[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@3da9df53] 204.8 Mb > - lund1051_resampled.tif[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@141b7d8d] 204.8 Mb > - CLIJ2_minimumOfTouchingNeighbors_result143[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@3dff54c8] 5.9 kb > - CLIJ2_greaterOrEqualConstant_result152[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@637a5492] 5.9 kb > - CLIJ2_excludeLabels_result153[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@105a5ce9] 204.8 Mb > - CLIJ2_maximumZProjection_result161[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@5f62ac7a] 984.6 kb > - CLIJ2_replaceIntensities_result149[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@187cea4a] 204.8 Mb > - CLIJ2_pushResultsTableColumn_result134[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@2993f313] 5.9 kb > - CLIJ2_replaceIntensities_result139[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@6b6c5fdc] 204.8 Mb > - CLIJ2_maximumZProjection_result160[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@21272fb7] 984.6 kb > - CLIJ2_replaceIntensities_result158[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@5ef6bf63] 204.8 Mb > - CLIJ2_replaceIntensities_result148[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@684bc4c5] 204.8 Mb > - CLIJ2_replaceIntensities_result159[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@61d0e4af] 204.8 Mb > - CLIJ2_smallerConstant_result146[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@799225b5] 5.9 kb > - CLIJ2_replaceIntensities_result135[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@12f48043] 204.8 Mb > - CLIJ2_smallerConstant_result137[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@24af0334] 5.9 kb > - CLIJ2_replaceIntensities_result144[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@42bc6e92] 204.8 Mb > - CLIJ2_smallerConstant_result155[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@2aeb44fd] 5.9 kb > - CLIJ2_replaceIntensities_result140[net.haesleinhuepf.clij.clearcl.ClearCLPeerPointer@1cab2f7b] 204.8 Mb > = 2.2 Gb >
Following methods are convenient for a proper visualization in a notebook:
function show(input, text) {
Ext.CLIJ2_maximumZProjection(input, max_projection);
Ext.CLIJ2_pull(max_projection);
setColor(100000);
drawString(text, 20, 20);
Ext.CLIJ2_release(max_projection);
}