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Register a new userInstance Segmentation for Whole Slide Imaging: End-to-End or Detect-Then-Segment
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Automatic instance segmentation of glomeruli within kidney Whole Slide Imaging (WSI) is essential for clinical research in renal pathology. In computer vision, the end-to-end instance segmentation methods (e.g., Mask-RCNN) have shown their advantages relative to detect-then-segment approaches by performing complementary detection and segmentation tasks simultaneously. As a result, the end-to-end Mask-RCNN approach has been the de facto standard method in recent glomerular segmentation studies, where downsampling and patch-based techniques are used to properly evaluate the high resolution images from WSI (e.g., >10,000x10,000 pixels on 40x). However, in high resolution WSI, a single glomerulus itself can be more than 1,000x1,000 pixels in original resolution which yields significant information loss when the corresponding features maps are downsampled via the Mask-RCNN pipeline. In this paper, we assess if the end-to-end instance segmentation framework is optimal for high-resolution WSI objects by comparing Mask-RCNN with our proposed detect-then-segment framework. Beyond such a comparison, we also comprehensively evaluate the performance of our detect-then-segment pipeline through: 1) two of the most prevalent segmentation backbones (U-Net and DeepLab_v3); 2) six different image resolutions (from 512x512 to 28x28); and 3) two different color spaces (RGB and LAB). Our detect-then-segment pipeline, with the DeepLab_v3 segmentation framework operating on previously detected glomeruli of 512x512 resolution, achieved a 0.953 dice similarity coefficient (DSC), compared with a 0.902 DSC from the end-to-end Mask-RCNN pipeline. Further, we found that neither RGB nor LAB color spaces yield better performance when compared against each other in the context of a detect-then-segment framework. Detect-then-segment pipeline achieved better segmentation performance compared with End-to-end method.
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Prostate cancer is the most prevalent cancer among men in Western countries, with 1.1 million new diagnoses every year. The gold standard for the diagnosis of prostate cancer is a pathologists evaluation of prostate tissue. To potentially assist pathologists deep-learning-based cancer detection systems have been developed. Many of the state-of-the-art models are patch-based convolutional neural networks, as the use of entire scanned slides is hampered by memory limitations on accelerator cards. Patch-based systems typically require detailed, pixel-level annotations for effective training. However, such annotations are seldom readily available, in contrast to the clinical reports of pathologists, which contain slide-level labels. As such, developing algorithms which do not require manual pixel-wise annotations, but can learn using only the clinical report would be a significant advancement for the field. In this paper, we propose to use a streaming implementation of convolutional layers, to train a modern CNN (ResNet-34) with 21 million parameters end-to-end on 4712 prostate biopsies. The method enables the use of entire biopsy images at high-resolution directly by reducing the GPU memory requirements by 2.4 TB. We show that modern CNNs, trained using our streaming approach, can extract meaningful features from high-resolution images without additional heuristics, reaching similar performance as state-of-the-art patch-based and multiple-instance learning methods. By circumventing the need for manual annotations, this approach can function as a blueprint for other tasks in histopathological diagnosis. The source code to reproduce the streaming models is available at https://github.com/DIAGNijmegen/pathology-streaming-pipeline .
Accelerated MRI shortens acquisition time by subsampling in the measurement k-space. Recovering a high-fidelity anatomical image from subsampled measurements requires close cooperation between two components: (1) a sampler that chooses the subsampling pattern and (2) a reconstructor that recovers images from incomplete measurements. In this paper, we leverage the sequential nature of MRI measurements, and propose a fully differentiable framework that jointly learns a sequential sampling policy simultaneously with a reconstruction strategy. This co-designed framework is able to adapt during acquisition in order to capture the most informative measurements for a particular target (Figure 1). Experimental results on the fastMRI knee dataset demonstrate that the proposed approach successfully utilizes intermediate information during the sampling process to boost reconstruction performance. In particular, our proposed method outperforms the current state-of-the-art learned k-space sampling baseline on up to 96.96% of test samples. We also investigate the individual and collective benefits of the sequential sampling and co-design strategies. Code and more visualizations are available at http://imaging.cms.caltech.edu/seq-mri
Hyperspectral images (HSIs) can provide rich spatial and spectral information with extensive application prospects. Recently, several methods using convolutional neural networks (CNNs) to reconstruct HSIs have been developed. However, most deep learning methods fit a brute-force mapping relationship between the compressive and standard HSIs. Thus, the learned mapping would be invalid when the observation data deviate from the training data. To recover the three-dimensional HSIs from two-dimensional compressive images, we present dual-camera equipment with a physics-informed self-supervising CNN method based on a coded aperture snapshot spectral imaging system. Our method effectively exploits the spatial-spectral relativization from the coded spectral information and forms a self-supervising system based on the camera quantum effect model. The experimental results show that our method can be adapted to a wide imaging environment with good performance. In addition, compared with most of the network-based methods, our system does not require a dedicated dataset for pre-training. Therefore, it has greater scenario adaptability and better generalization ability. Meanwhile, our system can be constantly fine-tuned and self-improved in real-life scenarios.
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.
End-to-end paradigms significantly improve the accuracy of various deep-learning-based computer vision models. To this end, tasks like object detection have been upgraded by replacing non-end-to-end components, such as removing non-maximum suppression by training with a set loss based on bipartite matching. However, such an upgrade is not applicable to instance segmentation, due to its significantly higher output dimensions compared to object detection. In this paper, we propose an instance segmentation Transformer, termed ISTR, which is the first end-to-end framework of its kind. ISTR predicts low-dimensional mask embeddings, and matches them with ground truth mask embeddings for the set loss. Besides, ISTR concurrently conducts detection and segmentation with a recurrent refinement strategy, which provides a new way to achieve instance segmentation compared to the existing top-down and bottom-up frameworks. Benefiting from the proposed end-to-end mechanism, ISTR demonstrates state-of-the-art performance even with approximation-based suboptimal embeddings. Specifically, ISTR obtains a 46.8/38.6 box/mask AP using ResNet50-FPN, and a 48.1/39.9 box/mask AP using ResNet101-FPN, on the MS COCO dataset. Quantitative and qualitative results reveal the promising potential of ISTR as a solid baseline for instance-level recognition. Code has been made available at: https://github.com/hujiecpp/ISTR.
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