Semi-supervised learning towards automated segmentation of PET images with limited annotations: Application to lymphoma patients

The time-consuming task of manual segmentation challenges routine systematic quantification of disease burden. Convolutional neural networks (CNNs) hold significant promise to reliably identify locations and boundaries of tumors from PET scans. We aimed to leverage the need for annotated data via semi-supervised approaches, with application to PET images of diffuse large B-cell lymphoma (DLBCL) and primary mediastinal large B-cell lymphoma (PMBCL). We analyzed 18F-FDG PET images of 292 patients with PMBCL (n=104) and DLBCL (n=188) (n=232 for training and validation, and n=60 for external testing). We employed FCM and MS losses for training a 3D U-Net with different levels of supervision: i) fully supervised methods with labeled FCM (LFCM) as well as Unified focal and Dice loss functions, ii) unsupervised methods with Robust FCM (RFCM) and Mumford-Shah (MS) loss functions, and iii) Semi-supervised methods based on FCM (RFCM+LFCM), as well as MS loss in combination with supervised Dice loss (MS+Dice). Unified loss function yielded higher Dice score (mean +/- standard deviation (SD)) (0.73 +/- 0.03; 95% CI, 0.67-0.8) compared to Dice loss (p-value<0.01). Semi-supervised (RFCM+alpha*LFCM) with alpha=0.3 showed the best performance, with a Dice score of 0.69 +/- 0.03 (95% CI, 0.45-0.77) outperforming (MS+alpha*Dice) for any supervision level (any alpha) (p<0.01). The best performer among (MS+alpha*Dice) semi-supervised approaches with alpha=0.2 showed a Dice score of 0.60 +/- 0.08 (95% CI, 0.44-0.76) compared to another supervision level in this semi-supervised approach (p<0.01). Semi-supervised learning via FCM loss (RFCM+alpha*LFCM) showed improved performance compared to supervised approaches. Considering the time-consuming nature of expert manual delineations and intra-observer variabilities, semi-supervised approaches have significant potential for automated segmentation workflows

Variational and deep learning segmentation of very-low-contrast X-ray computed tomography images of carbon/epoxy woven composites

The purpose of this work is to find an effective image segmentation method for lab-based micro-tomography (mu-CT) data of carbon fiber reinforced polymers (CFRP) with insufficient contrast-to-noise ratio. The segmentation is the first step in creating a realistic geometry (based on mu-CT) for finite element modelling of textile composites on meso-scale. Noise in X-ray imaging data of carbon/polymer composites forms a challenge for this segmentation due to the very low X-ray contrast between fiber and polymer and unclear fiber gradients. To the best of our knowledge, segmentation of mu-CT images of carbon/polymer textile composites with low resolution data (voxel size close to the fiber diameter) remains poorly documented. In this paper, we propose and evaluate different approaches for solving the segmentation problem: variational on the one hand and deep-learning-based on the other. In the author's view, both strategies present a novel and reliable ground for the segmentation of mu-CT data of CFRP woven composites. The predictions of both approaches were evaluated against a manual segmentation of the volume, constituting our "ground truth", which provides quantitative data on the segmentation accuracy. The highest segmentation accuracy (about 4.7% in terms of voxel-wise Dice similarity) was achieved using the deep learning approach with U-Net neural network

Box-supervised Instance Segmentation with Level Set Evolution

In contrast to the fully supervised methods using pixel-wise mask labels, box-supervised instance segmentation takes advantage of the simple box annotations, which has recently attracted a lot of research attentions. In this paper, we propose a novel single-shot box-supervised instance segmentation approach, which integrates the classical level set model with deep neural network delicately. Specifically, our proposed method iteratively learns a series of level sets through a continuous Chan-Vese energy-based function in an end-to-end fashion. A simple mask supervised SOLOv2 model is adapted to predict the instance-aware mask map as the level set for each instance. Both the input image and its deep features are employed as the input data to evolve the level set curves, where a box projection function is employed to obtain the initial boundary. By minimizing the fully differentiable energy function, the level set for each instance is iteratively optimized within its corresponding bounding box annotation. The experimental results on four challenging benchmarks demonstrate the leading performance of our proposed approach to robust instance segmentation in various scenarios. The code is available at: https://github.com/LiWentomng/boxlevelset.Comment: 17 page, 4figures, ECCV202

Task adapted reconstruction for inverse problems

The paper considers the problem of performing a task defined on a model parameter that is only observed indirectly through noisy data in an ill-posed inverse problem. A key aspect is to formalize the steps of reconstruction and task as appropriate estimators (non-randomized decision rules) in statistical estimation problems. The implementation makes use of (deep) neural networks to provide a differentiable parametrization of the family of estimators for both steps. These networks are combined and jointly trained against suitable supervised training data in order to minimize a joint differentiable loss function, resulting in an end-to-end task adapted reconstruction method. The suggested framework is generic, yet adaptable, with a plug-and-play structure for adjusting both the inverse problem and the task at hand. More precisely, the data model (forward operator and statistical model of the noise) associated with the inverse problem is exchangeable, e.g., by using neural network architecture given by a learned iterative method. Furthermore, any task that is encodable as a trainable neural network can be used. The approach is demonstrated on joint tomographic image reconstruction, classification and joint tomographic image reconstruction segmentation

Single-Image based unsupervised joint segmentation and denoising

In this work, we develop an unsupervised method for the joint segmentation and denoising of a single image. To this end, we combine the advantages of a variational segmentation method with the power of a self-supervised, single-image based deep learning approach. One major strength of our method lies in the fact, that in contrast to data-driven methods, where huge amounts of labeled samples are necessary, our model can segment an image into multiple meaningful regions without any training database. Further, we introduce a novel energy functional in which denoising and segmentation are coupled in a way that both tasks benefit from each other. The limitations of existing single-image based variational segmentation methods, which are not capable of dealing with high noise or generic texture, are tackled by this specific combination with self-supervised image denoising. We propose a unified optimisation strategy and show that, especially for very noisy images available in microscopy, our proposed joint approach outperforms its sequential counterpart as well as alternative methods focused purely on denoising or segmentation. Another comparison is conducted with a supervised deep learning approach designed for the same application, highlighting the good performance of our approach

A Novel Euler's Elastica based Segmentation Approach for Noisy Images via using the Progressive Hedging Algorithm

Euler's Elastica based unsupervised segmentation models have strong capability of completing the missing boundaries for existing objects in a clean image, but they are not working well for noisy images. This paper aims to establish a Euler's Elastica based approach that properly deals with random noises to improve the segmentation performance for noisy images. We solve the corresponding optimization problem via using the progressive hedging algorithm (PHA) with a step length suggested by the alternating direction method of multipliers (ADMM). Technically, all the simplified convex versions of the subproblems derived from the major framework of PHA can be obtained by using the curvature weighted approach and the convex relaxation method. Then an alternating optimization strategy is applied with the merits of using some powerful accelerating techniques including the fast Fourier transform (FFT) and generalized soft threshold formulas. Extensive experiments have been conducted on both synthetic and real images, which validated some significant gains of the proposed segmentation models and demonstrated the advantages of the developed algorithm