Bacteria Segmentation

Pixel-level colony masks

A U-Net produces per-pixel masks of bacterial colonies for the same 8 classes as the detection case.

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Algorithm

Stack
  • Python 3.8
  • Kedro
  • MLFlow
  • Pytorch
  • LabelMe
  • Albumentations
Dataset
  • 8 bacteria classes
  • Vector labeling
  • PNG/JPEG
  • Augmentation
Training
  • Unet
  • 100 epochs
  • 2x GTX1080TI

Model

Pipeline scheme