Just aware of Li and Malik paper "Amodal Instance Segmentation" https://arxiv.org/pdf/1604.08202.pdf. Just as Monsieur Jourdain was unaware that he was speaking prose, resolving overlapping chromosomes is an amodal segmentation, a task that instance segmentation algorithms are specifically designed to handle. A segmentation algorithm such an instance segmentation should be capable of generating overlapping masks by definition, for example:
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| COCO format overlapping masks (hand made). |
In our pre-print from 2017, the ground truth masks were of three kind: one for each chromosome and one for overlapping pixels:
Minor progress
- Masks simplification: one mask per chromosomes, no mask for overlapping domains.
- Use standardized grayscale images (mean and standard deviation inside the masks reunion)
As converting binary masks into coco format is a pain in the ass, we'll try to perform instance segmentation only with binary mask images. Making explicit masks corresponding to overlapping domain should not be necessary. So that one data looks like:
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| Standardized gray-scaled image (left) and its densitometric plot along a column. The two corresponding instances masks (M2 or M1) on the right. No binary mask for the overlapping domain of the two masks. The dataset used here is the 82146 dataset containing very low resolution images (52x52). |
