This plugin performs 2D/3D segmentation on grayscale images based on morphological operations and watershed transforms.
Morphological Segmentation is an ImageJ plugin that combines morphological operations, such as extended minima and morphological gradient, with watershed flooding algorithms to segment grayscale images of any type (8, 16 and 32-bit) in 2D and 3D.
Morphological Segmentation runs on any open grayscale image, single 2D image or (3D) stack. If no image is open when calling the plugin, an Open dialog will pop up.
The user can pan, zoom in and out, or scroll between slices (if the input image is a stack) in the main canvas as if it were any other ImageJ window. On the left side of the canvas there are three panels of parameters, one for the input image, one with the watershed parameters and one for the output options. All buttons, checkboxes and input panels contain a short explanation of their functionality that is displayed when the cursor lingers over them.
Image pre-processing: some pre-processing is included in the plugin to facilitate the segmentation task. However, other pre-preprocessing may be required depending on the input image. It is up to the user to decide what filtering may be most appropriate upstream.
First, you need to indicate the nature of the input image to process. This is a key parameter since the watershed algorithm is expecting an image where the boundaries of objects present high intensity values (usually as a result of a gradient or edge detection filtering).
You should select:
When selecting “Object Image”, an additional set of options is enabled to choose the type of gradient and radius (in pixels) to apply to the input image before starting the morphological operations. Finally, a checkbox allows displaying the gradient image instead of the input image in the main canvas of the plugin (only after running the watershed segmentation).
Finally, click on “Run” to launch the segmentation.
If your segmentation is taking too long or you want to stop it for any reason, you can do so by clicking on the same button (which should read “STOP” during that process).
Download the latest MorphoLibJ JAR into your ImageJ plugins folder and then restart ImageJ or simply apply the command Help>Refresh Menus. Then, you can call the plugin at Plugins > MorphoLibJ > Segmentation > Morphological Segmentation.
The latest release can be downloaded from here:
The source code can be found on GitHub.