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qAp / sartorius_cell_instance_segmentation_kaggle

Solution for Sartorius Cell Instance Segmentation Kaggle
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Rotational augmentation transforms for uvec #6

Closed qAp closed 2 years ago

qAp commented 2 years ago

Whole-image maps of:

are built up by computing them for individual cells, pasting them into the image frame, in order of descending of cell area.

There would be fewer computations if the whole-image uvec map was computed directly from the whole-map dtfm, but the resulting uvec map doesn't appear to mark out the cell boundaries well.

In addition, for rotational transforms during data augmentation, the uvec needs to be computed from the distance transform after the distance transform has been rotated. Its components cannot be simply treated like scalar maps that can be rotated the usual way using albumentations.

Because of these, it seems there are 2 options:

  1. During data augmentation, build all the needed maps from individual cell annotations. Pass individual cells' dtfm through the rotation, compute their uvec, then build up the whole-image uvec map from them. This might be too time-consuming.
  2. Rotate the whole-image uvec map using own rotation implementation, rotate all other maps using albumentations. This might restrict the variety of rotational transformations that can be used though.
qAp commented 2 years ago

https://github.com/qAp/sartorius_cell_instance_segmentation_kaggle/issues/2#issuecomment-992278340

It seems that the only thing that makes sense to pre-generate is the semantic segmentation, and everything else needs to be computed after the semantic segmentation has gone through whatever transforms are applied during data augmentation.

e.g. The distance transform and the discrete watershed energy can change for a point in the image after a perspective transform, or, the uvec can change after a rotational transform.

The only thing that seems to be preserved for a point in the image is the semantic segmentation. A point that belongs to cell nucleus stays that way regardless of the transforms applied, similarly for a point belonging to cell wall.