Revision as of 09:46, 11 October 2018 by Maarzt (talk | contribs) (Usage)
Labkit ()
Author Matthias Arzt
Update site Labkit
Maintainer Matthias Arzt
Source on GitHub

Labkit is a FIJI plugin for:

  • automatic image segmentation
  • labeling regions of an image

The automatic image segmentation functionality is comparable to Trainable Weka Segmenation, but it's better suited for large 3d images. And it has a nice Big Data Viewer based editor.


Labkit can be installed from the ImageJ update site: (For details on how to install an update site click here.)


Use ImageJ to open the image you want to create labels for. In ImageJ, select the image, and from the menu choose Plugins > Segmentation > Labkit.

Basic Usage

Follow these steps, expain how to segment an image:

  1. Open an image in ImageJ.
  2. Start Labkit by selecting "Plugins > Segmentation > Labkit" from the menu.
  3. Labkit should start and display the image. If it shows a black window instead of the image: Click S and adjust the contrast.
  4. Select "foreground" (In the side bar of Labkit). Select the pencil tool (top bar of Labkit) and draw on the image.
  5. Select "background" and the pencil tool, and mark some other region of the image as background.
  6. In the side bar of Labkit, under the heading "Segmentation" you will find an entry "Classifier #1". And next to it there is a play button (black triangle). Click it, to train the Classifier. After a moment you will see the automatic segmentation of your image.
  7. From Labkit's main menu select "Segmentation -> Show Segmentation Result in ImageJ", to export your segmentation into ImageJ.

Basic Navigation

  • ^ Ctrl+ Shift+mouse-wheel to zoom in and out
  • right-click+drag to move the image
  • left-click+drag to rotate a 3d image
  • mouse-wheel to scroll through the z-slices of a 3d image

Create Labels

When Space is pressed, while the mouse is over the image, a circle around the mouse pointer will appear.

  • Space+left click mark the pixels inside the circle
  • Space+right click remove the mark from the pixels inside the circle.
  • Space+mouse wheel change the size of the circle used to mark pixels.

By default pixels can be marked as "foreground" or "background". To switch between these two labels use N.