/cellSegmentation

cell segmentation

Primary LanguagePython

Cell Instance Segmentation

This repo was constructed for cell instance segmentation.

  1. run horizontalVerticalMap.py to save the horizontal and vertical maps.
  2. run train.py to train the model
  3. run inference.py to inference

Horizontal & Vertical Map

HOrizontalVertical

gradient

Model

There are 2 branches consisting of horizontalVertical(MSE loss) and segmentation(Dice + CE)

  • MSE loss: (l1)the loss of the horizontal and vertical map + (l2)the loss of the gradient of the horizontal and vertical map
  • Dice loss: sementic segmentation output(l3)
  • CE loss: sementic segmentation output(l4)

model

Loss

Loss = l1 + 2 * l2 + l3 + l4

Data Augmentation

Don't use flip or rotation