diff --git a/README.md b/README.md
index 708ea8a..868e8ba 100644
--- a/README.md
+++ b/README.md
@@ -8,11 +8,11 @@ Right now, this is very preliminary.
## Installation
Download the following files, removed the numbers from their file endings and put them all in a folder:
-* [clatlab-0.4.0.jar](https://github.com/clij/clatlab/releases/download/0.4.0/clatlab-0.4.0.jar)
+* [clatlab-0.5.0.jar](https://github.com/clij/clatlab/releases/download/0.5.0/clatlab-0.5.0.jar)
* [bridj-0.7.0.jar](https://sites.imagej.net/clij/jars/bridj-0.7.0.jar-20181201213334)
-* [clij_1.4.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij_-1.4.0.jar)
-* [clij-clearcl-0.10.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij-clearcl-0.10.0.jar)
-* [clij-core-1.4.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij-core-1.4.0.jar)
+* [clij_1.4.2.jar](https://github.com/clij/clij/releases/download/1.4.2/clij_-1.4.2.jar)
+* [clij-clearcl-0.10.1.jar](https://github.com/clij/clij/releases/download/1.4.2/clij-clearcl-0.10.1.jar)
+* [clij-core-1.4.2.jar](https://github.com/clij/clij/releases/download/1.4.2/clij-core-1.4.2.jar)
* [clij-coremem-0.6.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij-coremem-0.6.0.jar)
* [clij-legacy_-0.1.0.jar](https://github.com/clij/clij-legacy/releases/download/0.1.0/clij-legacy_-0.1.0.jar)
* [imagej-common-0.28.2.jar](https://sites.imagej.net/Java-8/jars/imagej-common-0.28.2.jar-20190516211613)
@@ -22,7 +22,9 @@ Download the following files, removed the numbers from their file endings and pu
* [scijava-common-2.77.0.jar](https://sites.imagej.net/Java-8/jars/scijava-common-2.76.1.jar-20181204141527)
* [ij-1.52p.jar](https://sites.imagej.net/Java-8/jars/ij-1.52p.jar-20190701230425)
* [imglib2-ij-2.0.0-beta-44.jar](https://sites.imagej.net/Java-8/jars/imglib2-ij-2.0.0-beta-44.jar-20181204141527)
-* [clij-advanced-filters_-0.11.0.jar](https://github.com/clij/clij-advanced-filters/releases/download/0.11.0/clij-advanced-filters_-0.11.0.jar)
+* [clij-advanced-filters_-0.12.4.jar](https://github.com/clij/clij-advanced-filters/releases/download/0.12.4/clij-advanced-filters_-0.12.4.jar)
+* [fiji-lib-2.1.2.jar](https://sites.imagej.net/Java-8/jars/fiji-lib-2.1.2.jar-20170530201750)
+
In your matlab script, specify _every_ individual jar file in this folder using `javaaddpath('folder/jarfile.jar').
It is recommended to do this in a utility function as [demonstrated here](https://github.com/clij/clatlab/blob/master/src/main/matlab/init_clatlab.m).
diff --git a/images/clablab-screenshot.png b/images/clablab-screenshot.png
index 31fd0aa..4bf113c 100644
Binary files a/images/clablab-screenshot.png and b/images/clablab-screenshot.png differ
diff --git a/pom.xml b/pom.xml
index 35c322d..ce2f899 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
net.haesleinhuepf
clatlab
- 0.4.0
+ 0.5.0
CLATLAB
CLIJ bridge to Matlab
@@ -27,12 +27,12 @@
net.haesleinhuepf
clij-core
- 1.4.0
+ 1.4.2
net.haesleinhuepf
clij-advanced-filters_
- 0.11.0
+ 0.12.4
diff --git a/src/main/matlab/init_clatlab.m b/src/main/matlab/init_clatlab.m
index 098fc5b..ee50b2d 100644
--- a/src/main/matlab/init_clatlab.m
+++ b/src/main/matlab/init_clatlab.m
@@ -17,11 +17,11 @@
if (exist('net.haesleinhuepf.clatlab.CLATLAB') ~= 8)
clatlab_folder = '../../../classpath/';
javaaddpath(strcat(clatlab_folder, 'ij-1.52p.jar'));
- javaaddpath(strcat(clatlab_folder, 'clatlab-0.4.0.jar'));
+ javaaddpath(strcat(clatlab_folder, 'clatlab-0.5.0.jar'));
javaaddpath(strcat(clatlab_folder, 'bridj-0.7.0.jar'));
- javaaddpath(strcat(clatlab_folder, 'clij_-1.4.0.jar'));
- javaaddpath(strcat(clatlab_folder, 'clij-clearcl-0.10.0.jar'));
- javaaddpath(strcat(clatlab_folder, 'clij-core-1.4.0.jar'));
+ javaaddpath(strcat(clatlab_folder, 'clij_-1.4.2.jar'));
+ javaaddpath(strcat(clatlab_folder, 'clij-clearcl-0.10.1.jar'));
+ javaaddpath(strcat(clatlab_folder, 'clij-core-1.4.2.jar'));
javaaddpath(strcat(clatlab_folder, 'clij-coremem-0.6.0.jar'));
javaaddpath(strcat(clatlab_folder, 'clij-legacy_-0.1.0.jar'));
javaaddpath(strcat(clatlab_folder, 'imagej-common-0.28.2.jar'));
@@ -30,8 +30,8 @@
javaaddpath(strcat(clatlab_folder, 'jocl-2.0.1.jar'));
javaaddpath(strcat(clatlab_folder, 'scijava-common-2.76.1.jar'));
javaaddpath(strcat(clatlab_folder, 'imglib2-ij-2.0.0-beta-44.jar'));
- javaaddpath(strcat(clatlab_folder, 'clij-advanced-filters_-0.11.0.jar'));
-
+ javaaddpath(strcat(clatlab_folder, 'clij-advanced-filters_-0.12.4.jar'));
+ javaaddpath(strcat(clatlab_folder, 'fiji-lib-2.1.2.jar'));
% import and initialize CLATLAB
diff --git a/src/main/matlab/segmentation.m b/src/main/matlab/segmentation.m
index 339dad4..3df0872 100644
--- a/src/main/matlab/segmentation.m
+++ b/src/main/matlab/segmentation.m
@@ -38,15 +38,16 @@
blurred = clijx.create(input);
thresholded = clijx.create(input);
labelled = clijx.create(input);
+labelled_without_edges = clijx.create(input);
% blur, threshold and label the image
clijx.blur(input, blurred, 5, 5, 0);
clijx.automaticThreshold(blurred, thresholded, "Otsu");
clijx.connectedComponentsLabeling(thresholded, labelled);
-
+clijx.excludeLabelsOnEdges(labelled, labelled_without_edges);
% pull result back from GPU and show it next to input
-result = clijx.pullMat(labelled);
+result = clijx.pullMat(labelled_without_edges);
number_of_found_objects = clijx.maximumOfAllPixels(labelled);
lookuptable = rand(number_of_found_objects, 3);
subplot(1,2,2), imshow(result, lookuptable);
@@ -57,3 +58,5 @@
thresholded.close();
labelled.close();
+
+
diff --git a/src/main/matlab/spotDetection3D.m b/src/main/matlab/spotDetection3D.m
index 9d69965..bd442da 100644
--- a/src/main/matlab/spotDetection3D.m
+++ b/src/main/matlab/spotDetection3D.m
@@ -92,7 +92,7 @@
scatter3(points(1,:), points(2,:), points(3,:))
% visualise data set as maximum projection
-maximumProjected = clx.create(processingSize(1:2), backgroundSubtracted.getNativeType());
+maximumProjected = clijx.create(processingSize(1:2), backgroundSubtracted.getNativeType());
clijx.maximumZProjection(backgroundSubtracted, maximumProjected);
figure
imshow(clijx.pullMat(maximumProjected), [0 250]);
@@ -111,5 +111,6 @@
z = points(3,:);
tri = delaunay(x, y, z)
%trimesh(tri, x, y, z);
+figure;
trisurf(tri, x, y, z,'FaceAlpha',0.3)