Add text labels for classes and IDs to whole images and objects within

ID tags
  • rapid manual labeling of IDs

  • automatic detection of QR codes

  • manual labeling of unsuccessful detections


Manual and automatic placement of landmarks, pseudo-landmarks and other annotations for geometric morphometrics

Stickleback landmarks
  • place landmarks on stained stickleback

  • automatic size correction

Object detection and counting#

Detecting many small objects against a uniform background for counting, and collect some simple traits from each object

Fluorescence traits in algae
  • cell segmentation and counting

  • extraction of shape and pattern traits from individual cells

Isopod counting
  • count small critters

  • quantify size and pigmentation

  • automatic size/color correction

Snail counting
  • count small freshwater snails

  • measure size and pigmentation

✨ Cichlid teeth
  • segment teeth against dark and light backgrounds

  • extract shape features

Measure worm length
  • find circles (well plates) in images

  • detect worm within circle, and measure length


Collect high dimensional traits from single specimens in high resolution images, e.g., tangible and abstract shape and color pattern / texture features

Stickleback armor plate measurement
  • thresholding of armor plates

  • extract size and shape

✨ Damselfly morphology
  • create training data

  • segment the whole body and body parts using deep learning

  • extract shape and texture traits from each part

Video analysis#

Tracking of individuals from videos with a static background

Motion tracking
  • mapping out predator-prey interactions between isopods and fish