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.
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.
Follow these steps, expain how to segment an image:
- Open an image in ImageJ.
- Start Labkit by selecting "Plugins > Segmentation > Labkit" from the menu.
- Labkit should start and display the image. If it shows a black window instead of the image: Click S and adjust the contrast.
- Select "foreground" (In the side bar of Labkit). Select the pencil tool (top bar of Labkit) and draw on the image.
- Select "background" and the pencil tool, and mark some other region of the image as background.
- 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.
- From Labkit's main menu select "Segmentation -> Show Segmentation Result in ImageJ", to export your segmentation into ImageJ.
- ^ 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
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.