Uncertainty-Aware Contour Proposal Networks for Cell Segmentation in Multi-Modality High-Resolution Microscopy Images

Eric Upschulte, Stefan Harmeling, Katrin Amunts, Timo Dickscheid

Keywords: cell, segmentation, detection, celldetection, microscopy, cpn, deep, learning, resnet, resnext, contour, proposal, network

TL;DR: We propose an uncertainty-aware Contour Proposal Network for cell segmentation in multi-modality high-resolution microscopy images.

Abstract:

We present a simple framework for cell segmentation, based on uncertainty-aware Contour Proposal Networks (CPNs).
It is designed to provide high segmentation accuracy while remaining computationally efficient, which makes it an ideal solution for high throughput microscopy applications.
Each predicted cell is provided with four uncertainty estimations that give information about the localization accuracy of the detected cell boundaries.
Such additional insights are valuable for downstream single-cell analysis in microscopy image-based biology and biomedical research.
In the context of the NeurIPS 22 Cell Segmentation Challenge, the proposed solution is shown to generalize well in a multi-modality setting, while respecting domain-specific requirements such as focusing on specific cell types.
Without an ensemble or test-time augmentation the method achieves an F1 score of $0.8986$ on the challenge's validation set.