Quantitative image analysis often depends on accurate classification of pixels through a segmentation process. However, imaging artifacts such as the partial volume effect and sensor noise complicate the classification process. These effects increase the pixel intensity variance of each constituent class, causing intensities from one class to overlap with another. This increased variance makes threshold based segmentation methods insufficient due to ambiguous overlap regions in the pixel intensity distributions. The class ambiguity becomes even more complex for systems with more than two constituents, such as unsaturated moist granular media. In this paper, we propose an image processing workflow that improves segmentation accuracy for multiphase systems. First, the ambiguous transition regions between classes are identified and removed, which allows for global thresholding of single-class regions. Then the transition regions are classified using a distance function, and finally both segmentations are combined into one classified image. This workflow includes three methodologies for identifying transition pixels and we demonstrate on a variety of synthetic images that these approaches are able to accurately separate the ambiguous transition pixels from the single-class regions. For situations with typical amounts of image noise, misclassification errors and area differences calculated between each class of the synthetic images and the resultant segmented images range from 0.69-1.48% and 0.01-0.74%, respectively, showing the segmentation accuracy of this approach. We demonstrate that we are able to accurately segment x-ray microtomography images of moist granular media using these computationally efficient methodologies.
Recent work has demonstrated that volumetric scene representations combined with differentiable volume rendering can enable photo-realistic rendering for challenging scenes that mesh reconstruction fails on. However, these methods entangle geometry and appearance in a "black-box" volume that cannot be edited. Instead, we present an approach that explicitly disentangles geometry--represented as a continuous 3D volume--from appearance--represented as a continuous 2D texture map. We achieve this by introducing a 3D-to-2D texture mapping (or surface parameterization) network into volumetric representations. We constrain this texture mapping network using an additional 2D-to-3D inverse mapping network and a novel cycle consistency loss to make 3D surface points map to 2D texture points that map back to the original 3D points. We demonstrate that this representation can be reconstructed using only multi-view image supervision and generates high-quality rendering results. More importantly, by separating geometry and texture, we allow users to edit appearance by simply editing 2D texture maps.
Volumetric imaging of samples using fluorescence microscopy plays an important role in various fields including physical, medical and life sciences. Here we report a deep learning-based volumetric image inference framework that uses 2D images that are sparsely captured by a standard wide-field fluorescence microscope at arbitrary axial positions within the sample volume. Through a recurrent convolutional neural network, which we term as Recurrent-MZ, 2D fluorescence information from a few axial planes within the sample is explicitly incorporated to digitally reconstruct the sample volume over an extended depth-of-field. Using experiments on C. Elegans and nanobead samples, Recurrent-MZ is demonstrated to increase the depth-of-field of a 63x/1.4NA objective lens by approximately 50-fold, also providing a 30-fold reduction in the number of axial scans required to image the same sample volume. We further illustrated the generalization of this recurrent network for 3D imaging by showing its resilience to varying imaging conditions, including e.g., different sequences of input images, covering various axial permutations and unknown axial positioning errors. Recurrent-MZ demonstrates the first application of recurrent neural networks in microscopic image reconstruction and provides a flexible and rapid volumetric imaging framework, overcoming the limitations of current 3D scanning microscopy tools.
Multiscale shape skeletonization on pixel adjacency graphs is an advanced intriguing research subject in the field of image processing, computer vision and data mining. The previous works in this area almost focused on the graph vertices. We proposed novel structured based graph morphological transformations based on edges opposite to the current node based transformations and used them for deploying skeletonization and reconstruction of infrared thermal images represented by graphs. The advantage of this method is that many widely used path based approaches become available within this definition of morphological operations. For instance, we use distance maps and image foresting transform (IFT) as two main path based methods are utilized for computing the skeleton of an image. Moreover, In addition, the open question proposed by Maragos et al (2013) about connectivity of graph skeletonization method are discussed and shown to be quite difficult to decide in general case.
For better clustering performance, appropriate representations are critical. Although many neural network-based metric learning methods have been proposed, they do not directly train neural networks to improve clustering performance. We propose a meta-learning method that train neural networks for obtaining representations such that clustering performance improves when the representations are clustered by the variational Bayesian (VB) inference with an infinite Gaussian mixture model. The proposed method can cluster unseen unlabeled data using knowledge meta-learned with labeled data that are different from the unlabeled data. For the objective function, we propose a continuous approximation of the adjusted Rand index (ARI), by which we can evaluate the clustering performance from soft clustering assignments. Since the approximated ARI and the VB inference procedure are differentiable, we can backpropagate the objective function through the VB inference procedure to train the neural networks. With experiments using text and image data sets, we demonstrate that our proposed method has a higher adjusted Rand index than existing methods do.
The world is still struggling in controlling and containing the spread of the COVID-19 pandemic caused by the SARS-CoV-2 virus. The medical conditions associated with SARS-CoV-2 infections have resulted in a surge in the number of patients at clinics and hospitals, leading to a significantly increased strain on healthcare resources. As such, an important part of managing and handling patients with SARS-CoV-2 infections within the clinical workflow is severity assessment, which is often conducted with the use of chest x-ray (CXR) images. In this work, we introduce COVID-Net CXR-S, a convolutional neural network for predicting the airspace severity of a SARS-CoV-2 positive patient based on a CXR image of the patient's chest. More specifically, we leveraged transfer learning to transfer representational knowledge gained from over 16,000 CXR images from a multinational cohort of over 15,000 patient cases into a custom network architecture for severity assessment. Experimental results with a multi-national patient cohort curated by the Radiological Society of North America (RSNA) RICORD initiative showed that the proposed COVID-Net CXR-S has potential to be a powerful tool for computer-aided severity assessment of CXR images of COVID-19 positive patients. Furthermore, radiologist validation on select cases by two board-certified radiologists with over 10 and 19 years of experience, respectively, showed consistency between radiologist interpretation and critical factors leveraged by COVID-Net CXR-S for severity assessment. While not a production-ready solution, the ultimate goal for the open source release of COVID-Net CXR-S is to act as a catalyst for clinical scientists, machine learning researchers, as well as citizen scientists to develop innovative new clinical decision support solutions for helping clinicians around the world manage the continuing pandemic.
Despite exciting progress in pre-training for visual-linguistic (VL) representations, very few aspire to a small VL model. In this paper, we study knowledge distillation (KD) to effectively compress a transformer-based large VL model into a small VL model. The major challenge arises from the inconsistent regional visual tokens extracted from different detectors of Teacher and Student, resulting in the misalignment of hidden representations and attention distributions. To address the problem, we retrain and adapt the Teacher by using the same region proposals from Student's detector while the features are from Teacher's own object detector. With aligned network inputs, the adapted Teacher is capable of transferring the knowledge through the intermediate representations. Specifically, we use the mean square error loss to mimic the attention distribution inside the transformer block and present a token-wise noise contrastive loss to align the hidden state by contrasting with negative representations stored in a sample queue. To this end, we show that our proposed distillation significantly improves the performance of small VL models on image captioning and visual question answering tasks. It reaches 120.8 in CIDEr score on COCO captioning, an improvement of 5.1 over its non-distilled counterpart; and an accuracy of 69.8 on VQA 2.0, a 0.8 gain from the baseline. Our extensive experiments and ablations confirm the effectiveness of VL distillation in both pre-training and fine-tuning stages.
We review the broad variety of methods that have been proposed for anomaly detection in images. Most methods found in the literature have in mind a particular application. Yet we show that the methods can be classified mainly by the structural assumption they make on the "normal" image. Five different structural assumptions emerge. Our analysis leads us to reformulate the best representative algorithms by attaching to them an a contrario detection that controls the number of false positives and thus derive universal detection thresholds. By combining the most general structural assumptions expressing the background's normality with the best proposed statistical detection tools, we end up proposing generic algorithms that seem to generalize or reconcile most methods. We compare the six best representatives of our proposed classes of algorithms on anomalous images taken from classic papers on the subject, and on a synthetic database. Our conclusion is that it is possible to perform automatic anomaly detection on a single image.
Hashing methods have attracted much attention for large scale image retrieval. Some deep hashing methods have achieved promising results by taking advantage of the strong representation power of deep networks recently. However, existing deep hashing methods treat all hash bits equally. On one hand, a large number of images share the same distance to a query image due to the discrete Hamming distance, which raises a critical issue of image retrieval where fine-grained rankings are very important. On the other hand, different hash bits actually contribute to the image retrieval differently, and treating them equally greatly affects the retrieval accuracy of image. To address the above two problems, we propose the query-adaptive deep weighted hashing (QaDWH) approach, which can perform fine-grained ranking for different queries by weighted Hamming distance. First, a novel deep hashing network is proposed to learn the hash codes and corresponding class-wise weights jointly, so that the learned weights can reflect the importance of different hash bits for different image classes. Second, a query-adaptive image retrieval method is proposed, which rapidly generates hash bit weights for different query images by fusing its semantic probability and the learned class-wise weights. Fine-grained image retrieval is then performed by the weighted Hamming distance, which can provide more accurate ranking than the traditional Hamming distance. Experiments on four widely used datasets show that the proposed approach outperforms eight state-of-the-art hashing methods.
Standard segmentation of medical images based on full-supervised convolutional networks demands accurate dense annotations. Such learning framework is built on laborious manual annotation with restrict demands for expertise, leading to insufficient high-quality labels. To overcome such limitation and exploit massive weakly labeled data, we relaxed the rigid labeling requirement and developed a semi-supervised learning framework based on a teacher-student fashion for organ and lesion segmentation with partial dense-labeled supervision and supplementary loose bounding-box supervision which are easier to acquire. Observing the geometrical relation of an organ and its inner lesions in most cases, we propose a hierarchical organ-to-lesion (O2L) attention module in a teacher segmentor to produce pseudo-labels. Then a student segmentor is trained with combinations of manual-labeled and pseudo-labeled annotations. We further proposed a localization branch realized via an aggregation of high-level features in a deep decoder to predict locations of organ and lesion, which enriches student segmentor with precise localization information. We validated each design in our model on LiTS challenge datasets by ablation study and showed its state-of-the-art performance compared with recent methods. We show our model is robust to the quality of bounding box and achieves comparable performance compared with full-supervised learning methods.