A solution to the Sartorius Cell Instance Segmentation Kaggle

https://www.kaggle.com/c/sartorius-cell-instance-segmentation

Solution summary

1. Semantic segmentation by Unet.
2. Instance segmentation by further processing of semantic segmentation with Deep Watershed Transform.

Deep Watershed Transform Network:

Semantic segmentation (Unet)

1. To generate training target:

python seggit/data/scripts/make_semseg_target.py

2. To make a training run:

python seggit/training/run_segmentation.py

3. To make inference:

from seggit.cell_semantic_segmentation import SemanticSegmenter
segmenter = SemanticSegmenter(checkpoint_path='best.pth')
img, semseg = segmenter.predict('sample.png')

Direction Net (DN)

1. To generate training target:

python seggit/data/scripts/make_uvec.py

2. To make a training run:

python training/run_direction.py

Watershed Transform Net (WTN)

1. To generate training target:

python seggit/data/scripts/make_wngy.py

2. To make a training run:

python training/run_energy.py

Deep Watershed Transform end-to-end (DN + WTN = WN)

1. To make a training run:

python training/run_watershed.py

2. To make an inference:

from seggit.deep_watershed_transform import DeepWatershedTransform

dwt = DeepWatershedTransform(checkpoint_path='best.pth')
wngy = dwt.predict(img, semg)

Cell instance segmentation (Unet + WN)

To make an inference :

from seggit.cell_instance_segmentation import CellSegmenter

parser = argparse.ArgumentParser()
CellSegmenter.add_argparse_args(parser)
args = parser.parse_args()
args.pth_unet = 'best_unet.pth'
args.pth_wn = 'best_wn.pth'

segmenter = CellSegmenter(args)

img, instg = segmenter.predict('sample.png')

References

• [ods.ai] topcoders, 1st place solution

• @hengck23 [placeholder] my approach and results

• Deep Watershed Transform for Instance Segmentation

• https://github.com/min2209/dwt

• Segmentation Models Pytorch https://github.com/qubvel/segmentation_models.pytorch

• https://en.wikipedia.org/wiki/Distance_transform

• https://stackoverflow.com/questions/61716670/distance-transform-the-function-does-not-work-properly

• https://stackoverflow.com/questions/61204462/error-in-function-distancetransform-python-using-opencv-3-4-9

• https://github.com/MouseLand/cellpose

• https://github.com/YukangWang/TextField