TopoSemiSeg: Enforcing Topological Consistency for Semi-Supervised Segmentation of Histopathology Images

In computational pathology, segmenting densely distributed objects like glands and nuclei is crucial for downstream analysis. To alleviate the burden of obtaining pixel-wise annotations, semi-supervised learning methods learn from large amounts of unlabeled data. Nevertheless, existing semi-supervised methods overlook the topological information hidden in the unlabeled images and are thus prone to topological errors, e.g., missing or incorrectly merged/separated glands or nuclei. To address this issue, we propose TopoSemiSeg, the first semi-supervised method that learns the topological representation from unlabeled data. In particular, we propose a topology-aware teacher-student approach in which the teacher and student networks learn shared topological representations. To achieve this, we introduce topological consistency loss, which contains signal consistency and noise removal losses to ensure the learned representation is robust and focuses on true topological signals. Extensive experiments on public pathology image datasets show the superiority of our method, especially on topology-wise evaluation metrics. Code is available at https://github.com/Melon-Xu/TopoSemiSeg.

Topology-Aware Uncertainty for Image Segmentation

Segmentation of curvilinear structures such as vasculature and road networks is challenging due to relatively weak signals and complex geometry/topology. To facilitate and accelerate large scale annotation, one has to adopt semi-automatic approaches such as proofreading by experts. In this work, we focus on uncertainty estimation for such tasks, so that highly uncertain, and thus error-prone structures can be identified for human annotators to verify. Unlike most existing works, which provide pixel-wise uncertainty maps, we stipulate it is crucial to estimate uncertainty in the units of topological structures, e.g., small pieces of connections and branches. To achieve this, we leverage tools from topological data analysis, specifically discrete Morse theory (DMT), to first capture the structures, and then reason about their uncertainties. To model the uncertainty, we (1) propose a joint prediction model that estimates the uncertainty of a structure while taking the neighboring structures into consideration (inter-structural uncertainty); (2) propose a novel Probabilistic DMT to model the inherent uncertainty within each structure (intra-structural uncertainty) by sampling its representations via a perturb-and-walk scheme. On various 2D and 3D datasets, our method produces better structure-wise uncertainty maps compared to existing works.

Learning Topological Interactions for Multi-Class Medical Image Segmentation

Deep learning methods have achieved impressive performance for multi-class medical image segmentation. However, they are limited in their ability to encode topological interactions among different classes (e.g., containment and exclusion). These constraints naturally arise in biomedical images and can be crucial in improving segmentation quality. In this paper, we introduce a novel topological interaction module to encode the topological interactions into a deep neural network. The implementation is completely convolution-based and thus can be very efficient. This empowers us to incorporate the constraints into end-to-end training and enrich the feature representation of neural networks. The efficacy of the proposed method is validated on different types of interactions. We also demonstrate the generalizability of the method on both proprietary and public challenge datasets, in both 2D and 3D settings, as well as across different modalities such as CT and Ultrasound. Code is available at: https://github.com/TopoXLab/TopoInteraction

Del-Net: A Single-Stage Network for Mobile Camera ISP

The quality of images captured by smartphones is an important specification since smartphones are becoming ubiquitous as primary capturing devices. The traditional image signal processing (ISP) pipeline in a smartphone camera consists of several image processing steps performed sequentially to reconstruct a high quality sRGB image from the raw sensor data. These steps consist of demosaicing, denoising, white balancing, gamma correction, colour enhancement, etc. Since each of them are performed sequentially using hand-crafted algorithms, the residual error from each processing module accumulates in the final reconstructed signal. Thus, the traditional ISP pipeline has limited reconstruction quality in terms of generalizability across different lighting conditions and associated noise levels while capturing the image. Deep learning methods using convolutional neural networks (CNN) have become popular in solving many image-related tasks such as image denoising, contrast enhancement, super resolution, deblurring, etc. Furthermore, recent approaches for the RAW to sRGB conversion using deep learning methods have also been published, however, their immense complexity in terms of their memory requirement and number of Mult-Adds make them unsuitable for mobile camera ISP. In this paper we propose DelNet - a single end-to-end deep learning model - to learn the entire ISP pipeline within reasonable complexity for smartphone deployment. Del-Net is a multi-scale architecture that uses spatial and channel attention to capture global features like colour, as well as a series of lightweight modified residual attention blocks to help with denoising. For validation, we provide results to show the proposed Del-Net achieves compelling reconstruction quality.