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mrokuss committed Jul 10, 2024
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# Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures 🩻
# [ECCV 2024] Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures 🩻

## Overview
Welcome to the repository for the paper **"Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures"**! 🎉 This repository provides the code for the implementation of the Skeleton Recall Loss integrated within the popular nnUNet framework.
[![arXiv](https://img.shields.io/badge/arXiv-2404.03010-B31B1B.svg)](https://arxiv.org/abs/2404.03010)


## News/Updates:

- 📄 **7/24**: ECCV Acceptance
- 🥇 **9/23**: Top solution without additional data on the [ToothFairy challenge](https://toothfairy.grand-challenge.org/)
- 🪧 **8/23**: MedNeurIPS poster
- 🥇 **7/23**: Skeleton Recall won the [TopCoW challenge](https://topcow23.grand-challenge.org/)

## Introduction
Accurately segmenting thin tubular structures, such as vessels, nerves, roads, or cracks, is a crucial task in computer vision. Traditional deep learning-based segmentation approaches often struggle to preserve the connectivity of these structures. This paper introduces **Skeleton Recall Loss**, a novel loss function designed to enhance connectivity conservation in thin tubular structure segmentation without incurring massive computational overheads.

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#### Full Loss calculation:

$\mathcal{L} = \mathcal{L}_{Dice} + \mathcal{L}_{CE} + w \cdot \mathcal{L}_{SkelRecall}$
$$\mathcal{L} = \mathcal{L}_{Dice} + \mathcal{L}_{CE} + w \cdot \mathcal{L}_{SkelRecall}$$

You can change the weight of the additional Skeleton Recall Loss term by modifying the value of `self.weight_srec` in the [nnUNetTrainerSkeletonRecall](nnunetv2/training/nnUNetTrainer/variants/loss/nnUNetTrainerSkeletonRecall.py)

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