Set the effect as following:

    private WritableImage image = new WritableImage(1000, 1000);
    private ImageInput imageInput = new ImageInput(image);
        node.setEffect(imageInput);

Then update the image using PixelWriter for example in respond to mouse events:

            PixelWriter pixelWriter = image.getPixelWriter();

            pixelWriter.setColor(x, y, Color.BLACK);

Effect is not being updated.

To update effect you need to null its source and update it to the image again.