volkerh / labeleditor

LabelEditor

The LabelEditor is a JugLab creation aiming to close the gap between segmentation algorithms and user interaction in ImageJ2 / Fiji.

For basic usage instructions see this thread on image.sc.

Implementation

core

model

The heart of this project is a mechanism to tag any label of an ImgLabeling instance with tags. A tag is of type Object so it can be anything.

view

A color can be assigned to a tag in ARGBType representation. The tag LabelEditorTag.DEFAULT can be used to assign a color to all labels with no associated tag. Renderers implementing LabelEditorRenderer will be discovered via the SciJava Plugin mechanism and translate an ImgLabeling into a RandomAccessibleInterval<ARGBType> with reference to the assigned tags and tag colors.

controller

This project uses Scijava Behaviours to bundle interaction concepts and connect them to a specific LabelEditorInterface instance (e.g. BDV or BVV).

plugins

interfaces

• BigDataViewer: currently the main target interface
  • [TODO] bigdataviewer-ui-panel will be used to provide control over BDV and LabelEditor settings
• BigVolumeViewer: buggy proof of concept implementation

behaviours

• currently, all existing behaviours are accessible via right-click menu
• SelectionBehaviours work like any default selection model and uses the tags LabelEditorTag.FOCUS and LabelEditorTag.SELECTED
• ConflictSelectionBehaviours are deselecting conflicting labels on each selection
• ModificationBehaviours
  • delete a label
  • merge labels (assigns the label of the first one to the other selected ones)
  • [TODO] label division (watershed) (WIP)
  • [TODO] label merge
  • [TODO] fill holes
• export options like exporting the ImgLabeling index image
• [TODO] export ImgLabeling as image with one mask channel per label
• [TODO] compute label regions, show information in table

renderer

• DefaultLabelEditorRenderer: paints each pixel of a label with the color of the tag(s)
• BorderLabelEditorRenderer: paints only the outer pixels of a label with the color of the tag(s) (the implementation here needs to be improved)
• [TODO] render numbers next to each label section
• [TODO] render bounding box

applications

The following application can be tested by installing this update site in Fiji: https://sites.imagej.net/LabelEditor

• Objects Counter (IJ2): Runs threshold and CCA and displays the result in the LabelEditor

How to use the API

There is no real documentation yet, also no JavaDoc. Have a look at src/test/sc/fiji/labeleditor/howto to see how to integrate this project into your own implementation. There are also script examples here: src/main/resources/script-templates/ImageJ2/LabelEditor

Configuration

• [TODO] Make behaviors configurable / come up with config loading / saving

Future steps

• ask for community feedback, maybe move / split up repo into core / plugins / applications
• join forces with Labkit
• figure out how to move towards ROI integration

Integration efforts

• [ongoing] metaseg
• [ongoing] MoMA
• [planned] Labkit
• [planned] CLIJ