Projects#

Labeling#

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

ID tags

  • rapid manual labeling of IDs

QR-codes

  • automatic detection of QR codes

  • manual labeling of unsuccessful detections

Landmarks#

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

Stickleback landmarks

  • place landmarks on stained stickleback

  • automatic size correction

Gasterosteus aculeatus

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

Phytoplankton communities

Isopod counting

  • count small critters

  • quantify size and pigmentation

  • automatic size/color correction

Asellus aquaticus

Snail counting

  • count small freshwater snails

  • measure size and pigmentation

Potamopyrgus antipodarum

✨ Cichlid teeth

  • segment teeth against dark and light backgrounds

  • extract shape features

Chichlid communities

Measure worm length

  • find circles (well plates) in images

  • detect worm within circle, and measure length

Lumbriculus variegatus

Phenomics#

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

Gasterosteus aculeatus

✨ Damselfly morphology

  • create training data

  • segment the whole body and body parts using deep learning

  • extract shape and texture traits from each part

Ischnura elegans

Video analysis#

Tracking of individuals from videos with a static background

Motion tracking

  • mapping out predator-prey interactions between isopods and fish

Gasterosteus aculeatus + Asellus aquaticus