EMBL Course

code/imagej-macro/filter-objects.ijm

+// TODO: add user interface for opening a label image file (https://imagej.net/Script_Parameters)
+// TODO: add user interface for min and max area
+
+run("Region Morphometry");
+
+minArea = 0;
+maxArea = 200;
+
+// TODO: Duplicate the label image, in order not to loose the original one
+
+for ( i = 0; i < Table.size; ++i )
+{
+	area = Table.get( "Area", i );
+	label = Table.getString( "Label", i );
+
+	// TODO: Add some text output to tell the user what is happening...
+	if ( area < minArea || area > maxArea )
+	{
+		run("Replace/Remove Label(s)", "label(s)="+label+" final=0");
+	}
+}
+
+// TODO (Optional): Relabel the filtered label image such that labels start from 1 and none are missing
+
+
+
+

workshops/image-analysis-automation.md

+# Image analysis automation
+
+## Automated object filtering
+
+<img src='https://g.gravizo.com/svg?
+ digraph G {
+    shift [fontcolor=white,color=white];
+    label_image -> table [label="  measure_shape"];
+    table -> filtered_objects;
+    filtered_objects -> label_image [label="  remove"];
+}
+'/>
+
+### Activity: Automatically remove objects from label image
+
+- Open image: `xy_8bit_labels__four_objects.tif`
+- Devise code to automatically remove objects from the label image, e.g.
+	- Remove all cells larger than N pixels in area
+
+### Formative assessment
+
+