The objective of this work is to segment any arbitrary structures of interest (SOI) in 3D volumes by only annotating a single slice, (i.e. semi-automatic 3D segmentation). We show that high accuracy can be achieved by simply propagating the 2D slice segmentation with an affinity matrix between consecutive slices, which can be learnt in a self-supervised manner, namely slice reconstruction. Specifically, we compare the proposed framework, termed as Sli2Vol, with supervised approaches and two other unsupervised/ self-supervised slice registration approaches, on 8 public datasets (both CT and MRI scans), spanning 9 different SOIs. Without any parameter-tuning, the same model achieves superior performance with Dice scores (0-100 scale) of over 80 for most of the benchmarks, including the ones that are unseen during training. Our results show generalizability of the proposed approach across data from different machines and with different SOIs: a major use case of semi-automatic segmentation methods where fully supervised approaches would normally struggle. The source code will be made publicly available at //github.com/pakheiyeung/Sli2Vol.
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Recent developments related to generative models have made it possible to generate diverse high-fidelity images. In particular, layout-to-image generation models have gained significant attention due to their capability to generate realistic complex images containing distinct objects. These models are generally conditioned on either semantic layouts or textual descriptions. However, unlike natural images, providing auxiliary information can be extremely hard in domains such as biomedical imaging and remote sensing. In this work, we propose a multi-object generation framework that can synthesize images with multiple objects without explicitly requiring their contextual information during the generation process. Based on a vector-quantized variational autoencoder (VQ-VAE) backbone, our model learns to preserve spatial coherency within an image as well as semantic coherency between the objects and the background through two powerful autoregressive priors: PixelSNAIL and LayoutPixelSNAIL. While the PixelSNAIL learns the distribution of the latent encodings of the VQ-VAE, the LayoutPixelSNAIL is used to specifically learn the semantic distribution of the objects. An implicit advantage of our approach is that the generated samples are accompanied by object-level annotations. We demonstrate how coherency and fidelity are preserved with our method through experiments on the Multi-MNIST and CLEVR datasets; thereby outperforming state-of-the-art multi-object generative methods. The efficacy of our approach is demonstrated through application on medical imaging datasets, where we show that augmenting the training set with generated samples using our approach improves the performance of existing models.
This paper presents a novel unsupervised approach to reconstruct human shape and pose from noisy point cloud. Traditional approaches search for correspondences and conduct model fitting iteratively where a good initialization is critical. Relying on large amount of dataset with ground-truth annotations, recent learning-based approaches predict correspondences for every vertice on the point cloud; Chamfer distance is usually used to minimize the distance between a deformed template model and the input point cloud. However, Chamfer distance is quite sensitive to noise and outliers, thus could be unreliable to assign correspondences. To address these issues, we model the probability distribution of the input point cloud as generated from a parametric human model under a Gaussian Mixture Model. Instead of explicitly aligning correspondences, we treat the process of correspondence search as an implicit probabilistic association by updating the posterior probability of the template model given the input. A novel unsupervised loss is further derived that penalizes the discrepancy between the deformed template and the input point cloud conditioned on the posterior probability. Our approach is very flexible, which works with both complete point cloud and incomplete ones including even a single depth image as input. Our network is trained from scratch with no need to warm-up the network with supervised data. Compared to previous unsupervised methods, our method shows the capability to deal with substantial noise and outliers. Extensive experiments conducted on various public synthetic datasets as well as a very noisy real dataset (i.e. CMU Panoptic) demonstrate the superior performance of our approach over the state-of-the-art methods. Code can be found \url{//github.com/wangsen1312/unsupervised3dhuman.git}
This paper explores the use of self-supervised deep learning in medical imaging in cases where two scan modalities are available for the same subject. Specifically, we use a large publicly-available dataset of over 20,000 subjects from the UK Biobank with both whole body Dixon technique magnetic resonance (MR) scans and also dual-energy x-ray absorptiometry (DXA) scans. We make three contributions: (i) We introduce a multi-modal image-matching contrastive framework, that is able to learn to match different-modality scans of the same subject with high accuracy. (ii) Without any adaption, we show that the correspondences learnt during this contrastive training step can be used to perform automatic cross-modal scan registration in a completely unsupervised manner. (iii) Finally, we use these registrations to transfer segmentation maps from the DXA scans to the MR scans where they are used to train a network to segment anatomical regions without requiring ground-truth MR examples. To aid further research, our code will be made publicly available.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show that our proposed SSL methods can achieve a substantial improvement of up to 17.3% over state-of-the-art supervised learning approaches with 400 unlabeled CT scans.
In the last decade, numerous supervised deep learning approaches requiring large amounts of labeled data have been proposed for visual-inertial odometry (VIO) and depth map estimation. To overcome the data limitation, self-supervised learning has emerged as a promising alternative, exploiting constraints such as geometric and photometric consistency in the scene. In this study, we introduce a novel self-supervised deep learning-based VIO and depth map recovery approach (SelfVIO) using adversarial training and self-adaptive visual-inertial sensor fusion. SelfVIO learns to jointly estimate 6 degrees-of-freedom (6-DoF) ego-motion and a depth map of the scene from unlabeled monocular RGB image sequences and inertial measurement unit (IMU) readings. The proposed approach is able to perform VIO without the need for IMU intrinsic parameters and/or the extrinsic calibration between the IMU and the camera. estimation and single-view depth recovery network. We provide comprehensive quantitative and qualitative evaluations of the proposed framework comparing its performance with state-of-the-art VIO, VO, and visual simultaneous localization and mapping (VSLAM) approaches on the KITTI, EuRoC and Cityscapes datasets. Detailed comparisons prove that SelfVIO outperforms state-of-the-art VIO approaches in terms of pose estimation and depth recovery, making it a promising approach among existing methods in the literature.
Biomedical image segmentation is an important task in many medical applications. Segmentation methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling datasets of medical images requires significant expertise and time, and is infeasible at large scales. To tackle the lack of labeled data, researchers use techniques such as hand-engineered preprocessing steps, hand-tuned architectures, and data augmentation. However, these techniques involve costly engineering efforts, and are typically dataset-specific. We present an automated data augmentation method for medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans, focusing on the one-shot segmentation scenario -- a practical challenge in many medical applications. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transforms from the images, and use the model along with the labeled example to synthesize additional labeled training examples for supervised segmentation. Each transform is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. Augmenting the training of a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at //github.com/xamyzhao/brainstorm.
3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multiple versions of "ground truths". Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semi-supervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.
We address the problem of segmenting 3D multi-modal medical images in scenarios where very few labeled examples are available for training. Leveraging the recent success of adversarial learning for semi-supervised segmentation, we propose a novel method based on Generative Adversarial Networks (GANs) to train a segmentation model with both labeled and unlabeled images. The proposed method prevents over-fitting by learning to discriminate between true and fake patches obtained by a generator network. Our work extends current adversarial learning approaches, which focus on 2D single-modality images, to the more challenging context of 3D volumes of multiple modalities. The proposed method is evaluated on the problem of segmenting brain MRI from the iSEG-2017 and MRBrainS 2013 datasets. Significant performance improvement is reported, compared to state-of-art segmentation networks trained in a fully-supervised manner. In addition, our work presents a comprehensive analysis of different GAN architectures for semi-supervised segmentation, showing recent techniques like feature matching to yield a higher performance than conventional adversarial training approaches. Our code is publicly available at //github.com/arnab39/FewShot_GAN-Unet3D
Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.
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