added usage exampels for matlab

Author: haesleinhuepf

md/applyVectorFieldMD/readme.md

@@ -20,7 +20,7 @@ run("Blobs (25K)");
 input = getTitle();
 
 </pre>
-<a href="image_1587799043401.png"><img src="image_1587799043401.png" width="250" alt="blobs.gif"/></a>
+<a href="image_1587799043401.png"><img src="image_1587799043401.png" width="224" alt="blobs.gif"/></a>
 
 Create two images describing local shift
 
@@ -39,8 +39,8 @@ run("Gaussian Blur...", "sigma=15");
 run("Enhance Contrast", "saturated=0.35");
 
 </pre>
-<a href="image_1587799043590.png"><img src="image_1587799043590.png" width="250" alt="shiftX"/></a>
-<a href="image_1587799043603.png"><img src="image_1587799043603.png" width="250" alt="shiftY"/></a>
+<a href="image_1587799043590.png"><img src="image_1587799043590.png" width="224" alt="shiftX"/></a>
+<a href="image_1587799043603.png"><img src="image_1587799043603.png" width="224" alt="shiftY"/></a>
 
 ## Initialize GPU and push images to GPU memory
 
@@ -69,12 +69,12 @@ for (i = 0; i < 36; i += 6) {
 }
 
 </pre>
-<a href="image_1587799043898.png"><img src="image_1587799043898.png" width="250" alt="Angle 0 deg"/></a>
-<a href="image_1587799043963.png"><img src="image_1587799043963.png" width="250" alt="Angle 60 deg"/></a>
-<a href="image_1587799044037.png"><img src="image_1587799044037.png" width="250" alt="Angle 120 deg"/></a>
-<a href="image_1587799044125.png"><img src="image_1587799044125.png" width="250" alt="Angle 180 deg"/></a>
-<a href="image_1587799044220.png"><img src="image_1587799044220.png" width="250" alt="Angle 240 deg"/></a>
-<a href="image_1587799044278.png"><img src="image_1587799044278.png" width="250" alt="Angle 300 deg"/></a>
+<a href="image_1587799043898.png"><img src="image_1587799043898.png" width="224" alt="Angle 0 deg"/></a>
+<a href="image_1587799043963.png"><img src="image_1587799043963.png" width="224" alt="Angle 60 deg"/></a>
+<a href="image_1587799044037.png"><img src="image_1587799044037.png" width="224" alt="Angle 120 deg"/></a>
+<a href="image_1587799044125.png"><img src="image_1587799044125.png" width="224" alt="Angle 180 deg"/></a>
+<a href="image_1587799044220.png"><img src="image_1587799044220.png" width="224" alt="Angle 240 deg"/></a>
+<a href="image_1587799044278.png"><img src="image_1587799044278.png" width="224" alt="Angle 300 deg"/></a>
 
 Cleanup by the end
 

md/basics/readme.md

@@ -43,7 +43,7 @@ run("Cell Colony (31K)");
 input_image = getTitle();
 Ext.CLIJ2_push(input_image);
 </pre>
-<a href="image_1587650909426.png"><img src="image_1587650909426.png" width="250" alt="Cell_Colony.jpg"/></a>
+<a href="image_1587650909426.png"><img src="image_1587650909426.png" width="224" alt="Cell_Colony.jpg"/></a>
 
 The image is now named in the GPU like it its image on screen. We can ask the GPU to tell us 
 which images it knows right now: 
@@ -76,7 +76,7 @@ In order to get the `result` back from the GPU, we need to pull it:
 <pre class="highlight">
 Ext.CLIJ2_pull(result);
 </pre>
-<a href="image_1587650909598.png"><img src="image_1587650909598.png" width="250" alt="CLIJ2_gaussianBlur2D_result114"/></a>
+<a href="image_1587650909598.png"><img src="image_1587650909598.png" width="224" alt="CLIJ2_gaussianBlur2D_result114"/></a>
 
 Furthermore, let's ask again which images are now in GPU memory:
 

md/benchmarking/readme.md

@@ -18,7 +18,7 @@ run("Image Sequence...", "open=C:/structure/data/unidesigner_groundtruth-drosoph
 input = getTitle();
 
 </pre>
-<a href="image_1587649616046.png"><img src="image_1587649616046.png" width="250" alt="raw"/></a>
+<a href="image_1587649616046.png"><img src="image_1587649616046.png" width="224" alt="raw"/></a>
 
 ## Measure processing time on the CPU
 
@@ -51,7 +51,7 @@ for (i = 1; i <= 10; i++) {
 > CPU mean filter no 9 took 9580 msec
 > CPU mean filter no 10 took 11088 msec
 </pre>
-<a href="image_1587649708300.png"><img src="image_1587649708300.png" width="250" alt="raw"/></a>
+<a href="image_1587649708300.png"><img src="image_1587649708300.png" width="224" alt="raw"/></a>
 
 ## Measure processing time on the GPU
 We perform the same strategy to measure processing time on the GPU. As the performance of
@@ -141,7 +141,7 @@ print("Pulling one image from the GPU took " + (getTime() - time) + " msec");
 <pre>
 > Pulling one image from the GPU took 127 msec
 </pre>
-<a href="image_1587649715555.png"><img src="image_1587649715555.png" width="250" alt="CLIJ2_mean3DBox_result9"/></a>
+<a href="image_1587649715555.png"><img src="image_1587649715555.png" width="224" alt="CLIJ2_mean3DBox_result9"/></a>
 
 For documentation purposes, we should also report which GPU was used
 

md/binary_processing/readme.md

@@ -29,7 +29,7 @@ run("Crop", " ");
 input = getTitle();
 
 </pre>
-<a href="image_1587651111934.png"><img src="image_1587651111934.png" width="250" alt="embryos.jpg"/></a>
+<a href="image_1587651111934.png"><img src="image_1587651111934.png" width="224" alt="embryos.jpg"/></a>
 
 Initialize GPU and push image to GPU memory
 
@@ -58,7 +58,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_thresholdOtsu">CLIJ2_th
 Ext.CLIJ2_pull(thresholded);
 
 </pre>
-<a href="image_1587651114252.png"><img src="image_1587651114252.png" width="250" alt="CLIJ2_thresholdOtsu_result116"/></a>
+<a href="image_1587651114252.png"><img src="image_1587651114252.png" width="224" alt="CLIJ2_thresholdOtsu_result116"/></a>
 
 ## Binary opening using erosion and dilation
 We do binary opening by hand: It consists of binary erosion and dilation, applied twice each.
@@ -71,7 +71,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_erodeBox">CLIJ2_erodeBo
 // show intermediate result
 Ext.CLIJ2_pull(intermediate_result);
 </pre>
-<a href="image_1587651114810.png"><img src="image_1587651114810.png" width="250" alt="CLIJ2_erodeBox_result118"/></a>
+<a href="image_1587651114810.png"><img src="image_1587651114810.png" width="224" alt="CLIJ2_erodeBox_result118"/></a>
 
 
 <pre class="highlight">
@@ -82,7 +82,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_dilateBox">CLIJ2_dilate
 Ext.CLIJ2_pull(opening_result);
 
 </pre>
-<a href="image_1587651115369.png"><img src="image_1587651115369.png" width="250" alt="CLIJ2_dilateBox_result119"/></a>
+<a href="image_1587651115369.png"><img src="image_1587651115369.png" width="224" alt="CLIJ2_dilateBox_result119"/></a>
 
 ## Binary closing
 For binary closing and opening, on can also call methods directly: 
@@ -95,7 +95,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_closingBox">CLIJ2_closi
 Ext.CLIJ2_pull(closing_result);
 
 </pre>
-<a href="image_1587651115444.png"><img src="image_1587651115444.png" width="250" alt="CLIJ2_closingBox_result120"/></a>
+<a href="image_1587651115444.png"><img src="image_1587651115444.png" width="224" alt="CLIJ2_closingBox_result120"/></a>
 
 ## Fill holes
 It is also possible to fill holes:
@@ -106,7 +106,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_binaryFillHoles">CLIJ2_
 Ext.CLIJ2_pullBinary(holes_filled);
 
 </pre>
-<a href="image_1587651118709.png"><img src="image_1587651118709.png" width="250" alt="CLIJ2_binaryFillHoles_result121"/></a>
+<a href="image_1587651118709.png"><img src="image_1587651118709.png" width="224" alt="CLIJ2_binaryFillHoles_result121"/></a>
 
 ## Edge detection
 We can retrieve an edge image like this:
@@ -117,7 +117,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_binaryEdgeDetection">CL
 Ext.CLIJ2_pullBinary(edges);
 
 </pre>
-<a href="image_1587651119241.png"><img src="image_1587651119241.png" width="250" alt="CLIJ2_binaryEdgeDetection_result122"/></a>
+<a href="image_1587651119241.png"><img src="image_1587651119241.png" width="224" alt="CLIJ2_binaryEdgeDetection_result122"/></a>
 
 Finally, always clean up:
 

md/blur/readme.md

@@ -19,7 +19,7 @@ run("Invert LUT");
 input = getTitle();
 
 </pre>
-<a href="image_1587651220246.png"><img src="image_1587651220246.png" width="250" alt="blobs.gif"/></a>
+<a href="image_1587651220246.png"><img src="image_1587651220246.png" width="224" alt="blobs.gif"/></a>
 
 Init GPU
  and push image data to GPU
@@ -45,7 +45,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_gaussianBlur3D">CLIJ2_g
 Ext.CLIJ2_pull(blurred);
 
 </pre>
-<a href="image_1587651221795.png"><img src="image_1587651221795.png" width="250" alt="CLIJ2_gaussianBlur3D_result125"/></a>
+<a href="image_1587651221795.png"><img src="image_1587651221795.png" width="224" alt="CLIJ2_gaussianBlur3D_result125"/></a>
 
 Cleanup by the end
 

md/clij1_clij2_combination/readme.md

@@ -23,8 +23,8 @@ original = getTitle();
 newImage("background", "16-bit ramp", width, height, slices);
  background = getTitle();
 </pre>
-<a href="image_1587651657700.png"><img src="image_1587651657700.png" width="250" alt="original"/></a>
-<a href="image_1587651657761.png"><img src="image_1587651657761.png" width="250" alt="background"/></a>
+<a href="image_1587651657700.png"><img src="image_1587651657700.png" width="224" alt="original"/></a>
+<a href="image_1587651657761.png"><img src="image_1587651657761.png" width="224" alt="background"/></a>
 
 ## Initialize GPU and push image data to GPU memory
 
@@ -60,7 +60,7 @@ Ext.CLIJ2_pull(originalWithBackground);
 run("Invert LUT"); 
 
 </pre>
-<a href="image_1587651657842.png"><img src="image_1587651657842.png" width="250" alt="originalWithBackground"/></a>
+<a href="image_1587651657842.png"><img src="image_1587651657842.png" width="224" alt="originalWithBackground"/></a>
 
 Clean up finally using CLIJ
 

md/compare_workflows/readme.md

@@ -33,9 +33,9 @@ run("Convert to Mask");
 
 end_time_imagej = getTime();
 </pre>
-<a href="image_1587651731709.png"><img src="image_1587651731709.png" width="250" alt="input_imagej"/></a>
-<a href="image_1587651732124.png"><img src="image_1587651732124.png" width="250" alt="background_subtracted_imagej"/></a>
-<a href="image_1587651733133.png"><img src="image_1587651733133.png" width="250" alt="thresholded_imagej"/></a>
+<a href="image_1587651731709.png"><img src="image_1587651731709.png" width="224" alt="input_imagej"/></a>
+<a href="image_1587651732124.png"><img src="image_1587651732124.png" width="224" alt="background_subtracted_imagej"/></a>
+<a href="image_1587651733133.png"><img src="image_1587651733133.png" width="224" alt="thresholded_imagej"/></a>
 
 
 Now we run the same workflow with CLIJ
@@ -69,9 +69,9 @@ Ext.CLIJ2_pullBinary(thresholded_clij);
 end_time_clij = getTime();
 
 </pre>
-<a href="image_1587651734937.png"><img src="image_1587651734937.png" width="250" alt="Lund_MAX_001300.tif"/></a>
-<a href="image_1587651735364.png"><img src="image_1587651735364.png" width="250" alt="background_subtracted_clij"/></a>
-<a href="image_1587651735950.png"><img src="image_1587651735950.png" width="250" alt="thresholded_clij"/></a>
+<a href="image_1587651734937.png"><img src="image_1587651734937.png" width="224" alt="Lund_MAX_001300.tif"/></a>
+<a href="image_1587651735364.png"><img src="image_1587651735364.png" width="224" alt="background_subtracted_clij"/></a>
+<a href="image_1587651735950.png"><img src="image_1587651735950.png" width="224" alt="thresholded_clij"/></a>
 
 The results look similar. There are difference because the 
 implementation of ImageJ background subtraction is close to but
@@ -121,15 +121,15 @@ in 32-bit because 8-bit images don't support negative values.
 imageCalculator("Subtract create 32-bit", "background_subtracted_imagej", background_subtracted_clij);
 
 </pre>
-<a href="image_1587651736256.png"><img src="image_1587651736256.png" width="250" alt="Result of background_subtracted_imagej"/></a>
+<a href="image_1587651736256.png"><img src="image_1587651736256.png" width="224" alt="Result of background_subtracted_imagej"/></a>
 
 ## Visual differences between thresholded images
 
 <pre class="highlight">
 imageCalculator("Subtract create 32-bit", "thresholded_imagej", thresholded_clij);
 
 </pre>
-<a href="image_1587651736902.png"><img src="image_1587651736902.png" width="250" alt="Result of thresholded_imagej"/></a>
+<a href="image_1587651736902.png"><img src="image_1587651736902.png" width="224" alt="Result of thresholded_imagej"/></a>
 
 This confirms visually our assumption: The background_subtracted images 
 are a bit different while the binary result images are not.

md/crop_and_paste/readme.md

@@ -18,7 +18,7 @@ run("Invert LUT");
 input = getTitle();
 
 </pre>
-<a href="image_1587652041130.png"><img src="image_1587652041130.png" width="250" alt="blobs.gif"/></a>
+<a href="image_1587652041130.png"><img src="image_1587652041130.png" width="224" alt="blobs.gif"/></a>
 
 ## Initialize GPU and push image to GPU memory
 
@@ -44,7 +44,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_crop2D">CLIJ2_crop2D</a
 Ext.CLIJ2_pull(cropped);
 
 </pre>
-<a href="image_1587652041252.png"><img src="image_1587652041252.png" width="250" alt="CLIJ2_crop2D_result136"/></a>
+<a href="image_1587652041252.png"><img src="image_1587652041252.png" width="224" alt="CLIJ2_crop2D_result136"/></a>
 
 ## Paste the image into another image
 We create an empty image and make a collage
@@ -73,7 +73,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_paste2D">CLIJ2_paste2D<
 Ext.CLIJ2_pull(collage);
 
 </pre>
-<a href="image_1587652041298.png"><img src="image_1587652041298.png" width="250" alt="CLIJ2_create2D_result137"/></a>
+<a href="image_1587652041298.png"><img src="image_1587652041298.png" width="224" alt="CLIJ2_create2D_result137"/></a>
 
 Clean up be the end
 

md/drosophila_max_cylinder_projection/readme.md

@@ -85,7 +85,7 @@ show(input_float, "Input image");
 > = 363.0 Mb
 >  
 </pre>
-<a href="image_1587652222401.png"><img src="image_1587652222401.png" width="250" alt="CLIJ2_maximumZProjection_result172"/></a>
+<a href="image_1587652222401.png"><img src="image_1587652222401.png" width="224" alt="CLIJ2_maximumZProjection_result172"/></a>
 
 ## Noise and background removal
 We use the difference-of-Gaussian (DoG) technique to remove noise and 
@@ -99,15 +99,15 @@ sigma2 = 6;
 Ext.<a href="https://clij.github.io/clij2-docs/reference_differenceOfGaussian3D">CLIJ2_differenceOfGaussian3D</a>(input_float, background_subtracted, sigma1, sigma1, 0, sigma2, sigma2, 0);
 show(background_subtracted, "Background subtracted");
 </pre>
-<a href="image_1587652222915.png"><img src="image_1587652222915.png" width="250" alt="CLIJ2_maximumZProjection_result174"/></a>
+<a href="image_1587652222915.png"><img src="image_1587652222915.png" width="224" alt="CLIJ2_maximumZProjection_result174"/></a>
 
 We remove negative and zero pixel intensities so that later only maxima above zero intensity are detected. 
 
 <pre class="highlight">
 Ext.<a href="https://clij.github.io/clij2-docs/reference_maximumImageAndScalar">CLIJ2_maximumImageAndScalar</a>(background_subtracted, positive_stack, 1.0);
 show(positive_stack, "Positive stack");
 </pre>
-<a href="image_1587652223595.png"><img src="image_1587652223595.png" width="250" alt="CLIJ2_maximumZProjection_result176"/></a>
+<a href="image_1587652223595.png"><img src="image_1587652223595.png" width="224" alt="CLIJ2_maximumZProjection_result176"/></a>
 
 ## Resampling
 All following transforms become mathematically easier to perform by resampling the
@@ -123,7 +123,7 @@ linearInterpolation = true;
 Ext.<a href="https://clij.github.io/clij2-docs/reference_resample">CLIJ2_resample</a>(positive_stack, resampled, resampleX, resampleY, resampleZ, linearInterpolation);
 show(resampled, "Resampled")
 </pre>
-<a href="image_1587652224025.png"><img src="image_1587652224025.png" width="250" alt="CLIJ2_maximumZProjection_result178"/></a>
+<a href="image_1587652224025.png"><img src="image_1587652224025.png" width="224" alt="CLIJ2_maximumZProjection_result178"/></a>
 
 ## Spatial trnansforms 
 Goal of this workflow is to perform a maximum projection from the center of the embryo to the surface. 
@@ -138,7 +138,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_resliceTop">CLIJ2_resli
 show(reslicedFromTop, "Resliced from top");
 
 </pre>
-<a href="image_1587652224173.png"><img src="image_1587652224173.png" width="250" alt="CLIJ2_maximumZProjection_result180"/></a>
+<a href="image_1587652224173.png"><img src="image_1587652224173.png" width="224" alt="CLIJ2_maximumZProjection_result180"/></a>
 
 ### Radial reslicing
 
@@ -156,7 +156,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_resliceRadial">CLIJ2_re
 show(radialResliced, "Radial projection");
 
 </pre>
-<a href="image_1587652224286.png"><img src="image_1587652224286.png" width="250" alt="CLIJ2_maximumZProjection_result182"/></a>
+<a href="image_1587652224286.png"><img src="image_1587652224286.png" width="224" alt="CLIJ2_maximumZProjection_result182"/></a>
 
 ### Reslicing from inside to outside
 
@@ -165,7 +165,7 @@ Ext.<a href="https://clij.github.io/clij2-docs/reference_resliceLeft">CLIJ2_resl
 show(reslicedFromLeft, "Resliced from inside to outside");
 
 </pre>
-<a href="image_1587652224403.png"><img src="image_1587652224403.png" width="250" alt="CLIJ2_maximumZProjection_result184"/></a>
+<a href="image_1587652224403.png"><img src="image_1587652224403.png" width="224" alt="CLIJ2_maximumZProjection_result184"/></a>
 
 ## Maximum projection
 
@@ -185,7 +185,7 @@ the image back from GPU memory to CPU memory.
 Ext.CLIJ_pull(maxProjected);
 
 </pre>
-<a href="image_1587652224510.png"><img src="image_1587652224510.png" width="250" alt="CLIJ2_maximumZProjection_result185"/></a>
+<a href="image_1587652224510.png"><img src="image_1587652224510.png" width="224" alt="CLIJ2_maximumZProjection_result185"/></a>
 
 For spot detection we use ImageJs `Find Maxima` method.
 
@@ -205,7 +205,7 @@ run("Flatten");
 <pre>
 > Number of spots found:2454
 </pre>
-<a href="image_1587652225764.png"><img src="image_1587652225764.png" width="250" alt="CLIJ2_maximumZProjection_result185-1"/></a>
+<a href="image_1587652225764.png"><img src="image_1587652225764.png" width="224" alt="CLIJ2_maximumZProjection_result185-1"/></a>
 
 # Performance evaluation
 Finally a time measurement. Note that performing this workflow with ImageJ macro markdown is slower 

md/filtering_in_graphs/readme.md

@@ -38,7 +38,7 @@ Ext.CLIJ2_pull(pointlist);
 zoom(10);
 
 </pre>
-<a href="image_1587654657082.png"><img src="image_1587654657082.png" width="250" alt="CLIJ2_create2D_result1-1"/></a>
+<a href="image_1587654657082.png"><img src="image_1587654657082.png" width="224" alt="CLIJ2_create2D_result1-1"/></a>
 
 ## Draw the spots labelled (1, 2, 3, ...) in 2D space
 
@@ -49,7 +49,7 @@ zoom(4);
 run("glasbey_on_dark");
 
 </pre>
-<a href="image_1587654657283.png"><img src="image_1587654657283.png" width="250" alt="CLIJ2_pointlistToLabelledSpots_result2-1"/></a>
+<a href="image_1587654657283.png"><img src="image_1587654657283.png" width="224" alt="CLIJ2_pointlistToLabelledSpots_result2-1"/></a>
 
 ## Partition the space between the points.
 
@@ -60,7 +60,7 @@ zoom(4);
 run("glasbey_on_dark");;
 
 </pre>
-<a href="image_1587654657475.png"><img src="image_1587654657475.png" width="250" alt="CLIJ2_labelVoronoiOctagon_result3-1"/></a>
+<a href="image_1587654657475.png"><img src="image_1587654657475.png" width="224" alt="CLIJ2_labelVoronoiOctagon_result3-1"/></a>
 
 ## Distribute a random measurement in space - with one outlier
 
@@ -76,7 +76,7 @@ Ext.CLIJ2_pull(measurement);
 zoom(10);
 
 </pre>
-<a href="image_1587654657605.png"><img src="image_1587654657605.png" width="250" alt="CLIJ2_pushArray_result4-1"/></a>
+<a href="image_1587654657605.png"><img src="image_1587654657605.png" width="224" alt="CLIJ2_pushArray_result4-1"/></a>
 
 ## Make a parametric image showing measurements in 2D space
 
@@ -88,7 +88,7 @@ setMinAndMax(0, 20);
 run("Fire");
 
 </pre>
-<a href="image_1587654657755.png"><img src="image_1587654657755.png" width="250" alt="CLIJ2_replaceIntensities_result5-1"/></a>
+<a href="image_1587654657755.png"><img src="image_1587654657755.png" width="224" alt="CLIJ2_replaceIntensities_result5-1"/></a>
 
 ## Calculate the median measurement for every node in graph, the median of its neighbors
 
@@ -108,7 +108,7 @@ setMinAndMax(0, 20);
 run("Fire");
 
 </pre>
-<a href="image_1587654657972.png"><img src="image_1587654657972.png" width="250" alt="CLIJ2_replaceIntensities_result5-2"/></a>
+<a href="image_1587654657972.png"><img src="image_1587654657972.png" width="224" alt="CLIJ2_replaceIntensities_result5-2"/></a>
 
 As you can see, the outlier is gone :-)
 

md/image_statistics/readme.md

@@ -18,7 +18,7 @@ run("Invert LUT");
 input = getTitle();
 
 </pre>
-<a href="image_1587652419772.png"><img src="image_1587652419772.png" width="250" alt="blobs-2.gif"/></a>
+<a href="image_1587652419772.png"><img src="image_1587652419772.png" width="224" alt="blobs-2.gif"/></a>
 
 ## Initialize GPU
  and push image data to GPU memory