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Register a new userNINEPINS: Nuclei Instance Segmentation with Point Annotations
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Deep learning-based methods are gaining traction in digital pathology, with an increasing number of publications and challenges that aim at easing the work of systematically and exhaustively analyzing tissue slides. These methods often achieve very high accuracies, at the cost of requiring large annotated datasets to train. This requirement is especially difficult to fulfill in the medical field, where expert knowledge is essential. In this paper we focus on nuclei segmentation, which generally requires experienced pathologists to annotate the nuclear areas in gigapixel histological images. We propose an algorithm for instance segmentation that uses pseudo-label segmentations generated automatically from point annotations, as a method to reduce the burden for pathologists. With the generated segmentation masks, the proposed method trains a modified version of HoVer-Net model to achieve instance segmentation. Experimental results show that the proposed method is robust to inaccuracies in point annotations and comparison with Hover-Net trained with fully annotated instance masks shows that a degradation in segmentation performance does not always imply a degradation in higher order tasks such as tissue classification.
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Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of nuclei using convolutional neural networks (CNNs) is described. In particular, since creating labeled volumes manually for training purposes is not practical due to the size and complexity of the 3D data sets, the paper describes a method for generating synthetic microscopy volumes based on a spatially constrained cycle-consistent adversarial network. The proposed method is tested on multiple real microscopy data sets and outperforms other commonly used segmentation techniques.
Medical image segmentation annotations suffer from inter- and intra-observer variations even among experts due to intrinsic differences in human annotators and ambiguous boundaries. Leveraging a collection of annotators opinions for an image is an interesting way of estimating a gold standard. Although training deep models in a supervised setting with a single annotation per image has been extensively studied, generalizing their training to work with datasets containing multiple annotations per image remains a fairly unexplored problem. In this paper, we propose an approach to handle annotators disagreements when training a deep model. To this end, we propose an ensemble of Bayesian fully convolutional networks (FCNs) for the segmentation task by considering two major factors in the aggregation of multiple ground truth annotations: (1) handling contradictory annotations in the training data originating from inter-annotator disagreements and (2) improving confidence calibration through the fusion of base models predictions. We demonstrate the superior performance of our approach on the ISIC Archive and explore the generalization performance of our proposed method by cross-dataset evaluation on the PH2 and DermoFit datasets.
We consider unsupervised cell nuclei segmentation in this paper. Exploiting the recently-proposed unpaired image-to-image translation between cell nuclei images and randomly synthetic masks, existing approaches, e.g., CycleGAN, have achieved encouraging results. However, these methods usually take a two-stage pipeline and fail to learn end-to-end in cell nuclei images. More seriously, they could lead to the lossy transformation problem, i.e., the content inconsistency between the original images and the corresponding segmentation output. To address these limitations, we propose a novel end-to-end unsupervised framework called Aligned Disentangling Generative Adversarial Network (AD-GAN). Distinctively, AD-GAN introduces representation disentanglement to separate content representation (the underling spatial structure) from style representation (the rendering of the structure). With this framework, spatial structure can be preserved explicitly, enabling a significant reduction of macro-level lossy transformation. We also propose a novel training algorithm able to align the disentangled content in the latent space to reduce micro-level lossy transformation. Evaluations on real-world 2D and 3D datasets show that AD-GAN substantially outperforms the other comparison methods and the professional software both quantitatively and qualitatively. Specifically, the proposed AD-GAN leads to significant improvement over the current best unsupervised methods by an average 17.8% relatively (w.r.t. the metric DICE) on four cell nuclei datasets. As an unsupervised method, AD-GAN even performs competitive with the best supervised models, taking a further leap towards end-to-end unsupervised nuclei segmentation.
Development of deep learning systems for biomedical segmentation often requires access to expert-driven, manually annotated datasets. If more than a single expert is involved in the annotation of the same images, then the inter-expert agreement is not necessarily perfect, and no single expert annotation can precisely capture the so-called ground truth of the regions of interest on all images. Also, it is not trivial to generate a reference estimate using annotations from multiple experts. Here we present a deep neural network, defined as U-Net-and-a-half, which can simultaneously learn from annotations performed by multiple experts on the same set of images. U-Net-and-a-half contains a convolutional encoder to generate features from the input images, multiple decoders that allow simultaneous learning from image masks obtained from annotations that were independently generated by multiple experts, and a shared low-dimensional feature space. To demonstrate the applicability of our framework, we used two distinct datasets from digital pathology and radiology, respectively. Specifically, we trained two separate models using pathologist-driven annotations of glomeruli on whole slide images of human kidney biopsies (10 patients), and radiologist-driven annotations of lumen cross-sections of human arteriovenous fistulae obtained from intravascular ultrasound images (10 patients), respectively. The models based on U-Net-and-a-half exceeded the performance of the traditional U-Net models trained on single expert annotations alone, thus expanding the scope of multitask learning in the context of biomedical image segmentation.
Instance segmentation methods often require costly per-pixel labels. We propose a method that only requires point-level annotations. During training, the model only has access to a single pixel label per object, yet the task is to output full segmentation masks. To address this challenge, we construct a network with two branches: (1) a localization network (L-Net) that predicts the location of each object; and (2) an embedding network (E-Net) that learns an embedding space where pixels of the same object are close. The segmentation masks for the located objects are obtained by grouping pixels with similar embeddings. At training time, while L-Net only requires point-level annotations, E-Net uses pseudo-labels generated by a class-agnostic object proposal method. We evaluate our approach on PASCAL VOC, COCO, KITTI and CityScapes datasets. The experiments show that our method (1) obtains competitive results compared to fully-supervised methods in certain scenarios; (2) outperforms fully- and weakly- supervised methods with a fixed annotation budget; and (3) is a first strong baseline for instance segmentation with point-level supervision.
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