LaRoMe
What a strange name !
LaRoME = Label + Region Of Interest + Measure
Label image (aka Count Masks): An image in which pixels of an object have all the same value. Each object has a unique value.
Measurement image: An image in which pixels of an object have all the same value, corresponding to a measurement (Area, Angle, Mean...)
Scripting
You can find a Macro language and a Groovy examples in the scripts folder.
Installation
You can install LaRoMe via the PTBIOP update site.
Help>Update..., Manage Update Sites, select PTBIOP in the list (cf image below), Apply changes, Restart Fiji.
ImageJ plugin
Plugins > BIOP > Image Analysis > ROIs >
run("Label image to ROIs")
From a Label Image(§), generate ROIs and add them to the ImageJ ROI Manager.
Macro Language, you can use run("Label image to ROIs"); as in the example code below :
if (nImages>0) run("Label image to ROIs");
run("ROIs to Label image", "")
From an Image and some ROIs, generates a Label Image.
Macro Language, you can use run("ROIs to Label image"); as in the example code below :
if ((nImages>0)&&( roiManager("count") > 0)) run("ROIs to Label image");
else if (roiManager("count") == 0) print("No existing ROIs to make Label Image");
else if (nImages==0) print("No open image to use as template for dimensions");
run("ROIs to Measurement Image", "column_name=Area");
From an Image, some ROIs and a selected Measurement generates a Measurement Image.
Measurement list encompass (change column_name ) : "Area", "Angle", "AngleVert","AR", "Circ.", "Major","Minor","Mean","Median","Mode","Min","Max", "Perim."
Angle measure is based on horizontal, the AngleVert measure is based on vertical (substracting 90 )
AR, Aspect Ratio = Major / Minor
Circ., Aspect Ratio = 4 * PI * Area / Perim.^2
Macro Language, you can use run("ROIs to Measurement Image"; as in the example code below:
run("ROIs to Measurement Image" , "column_name=Area pattern=[]");
With the lastest version (0.2) you can now use the ROI name with the option Pattern to define label (application for tracking or 3D-objects).
For example , using ijs-script
you can use Track-(\d*):.* to generate a label image per track.
