Gaussian Blur Subtraction

In this example we will use SciJava Ops to open an image, apply a gaussian blur and subtract the blurred image from the input image. This technique can be used to extract features, such as puncta, from a noisy background.

Here is a script using script parameters, runnable in Fiji’s Script Editor:

GroovyPython

#@ ImgPlus img
#@ Double (label="Sigma:", value=5.0) sigma
#@output ImgPlus result

import org.scijava.ops.api.OpEnvironment
import net.imglib2.type.numeric.real.FloatType

// build the Ops environment
ops = OpEnvironment.build();

// convert input ImgPlus image to float32
img = ops.op("convert.float32").input(img).apply();

// create gaussian blurred image
img_gauss = ops.op("filter.gauss").input(img, sigma).apply();

// subtract the input and blurred images
result = ops.op("create.img").input(img, new FloatType()).apply();
ops.op("math.sub").input(img, img_gauss).output(result).compute();