Ideas for the future development of SegEM


Here are some ideas and features I want to implement in the future.

Ideas and possible new features

  • Focused annotation of supervoxel graph
  • Use SegEM for answering biological questions
  • Improve usability using feedback from users


  • Write an efficent implementation of 3D-CNN for detecting membranes in EM images
  • Use marker-based waterbased to segement images based on result from CNN
  • Report voxel based-metrics as described in the ISBI challenge on 2D segmentation
  • Propose skeleton-based split-merger metric for better biological interpretability
  • Make skeleton-based volume reconstruction useable for intracellular stained data
  • Write methods to automatically detect contacts between cell pairs and inspect them in