Given earth imagery with spectral features on a terrain surface, this paper studies surface segmentation based on both explanatory features and surface topology. The problem is important in many spatial and spatiotemporal applications such as flood extent mapping in hydrology. The problem is uniquely challenging for several reasons: first, the size of earth imagery on a terrain surface is often much larger than the input of popular deep convolutional neural networks; second, there exists topological structure dependency between pixel classes on the surface, and such dependency can follow an unknown and non-linear distribution; third, there are often limited training labels. Existing methods for earth imagery segmentation often divide the imagery into patches and consider the elevation as an additional feature channel. These methods do not fully incorporate the spatial topological structural constraint within and across surface patches and thus often show poor results, especially when training labels are limited. Existing methods on semi-supervised and unsupervised learning for earth imagery often focus on learning representation without explicitly incorporating surface topology. In contrast, we propose a novel framework that explicitly models the topological skeleton of a terrain surface with a contour tree from computational topology, which is guided by the physical constraint (e.g., water flow direction on terrains). Our framework consists of two neural networks: a convolutional neural network (CNN) to learn spatial contextual features on a 2D image grid, and a graph neural network (GNN) to learn the statistical distribution of physics-guided spatial topological dependency on the contour tree. The two models are co-trained via variational EM. Evaluations on the real-world flood mapping datasets show that the proposed models outperform baseline methods in classification accuracy, especially when training labels are limited.
more »
« less
Deep Variational Instance Segmentation
Instance segmentation, which seeks to obtain both class and instance labels for
each pixel in the input image, is a challenging task in computer vision. State-ofthe-art algorithms often employ a search-based strategy, which first divides the
output image with a regular grid and generate proposals at each grid cell, then
the proposals are classified and boundaries refined. In this paper, we propose
a novel algorithm that directly utilizes a fully convolutional network (FCN) to
predict instance labels. Specifically, we propose a variational relaxation of instance
segmentation as minimizing an optimization functional for a piecewise-constant
segmentation problem, which can be used to train an FCN end-to-end. It extends
the classical Mumford-Shah variational segmentation algorithm to be able to handle
the permutation-invariant ground truth in instance segmentation. Experiments on
PASCAL VOC 2012 and the MSCOCO 2017 dataset show that the proposed
approach efficiently tackles the instance segmentation task. The source code and
trained models are released at https://github.com/jia2lin3yuan1/2020-instanceSeg.
more »
« less
- NSF-PAR ID:
- 10281811
- Date Published:
- Journal Name:
- Advances in neural information processing systems
- ISSN:
- 1049-5258
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
more » « less
Background Quantitative analysis of mitochondrial morphology plays important roles in studies of mitochondrial biology. The analysis depends critically on segmentation of mitochondria, the image analysis process of extracting mitochondrial morphology from images. The main goal of this study is to characterize the performance of convolutional neural networks (CNNs) in segmentation of mitochondria from fluorescence microscopy images. Recently, CNNs have achieved remarkable success in challenging image segmentation tasks in several disciplines. So far, however, our knowledge of their performance in segmenting biological images remains limited. In particular, we know little about their robustness, which defines their capability of segmenting biological images of different conditions, and their sensitivity, which defines their capability of detecting subtle morphological changes of biological objects.
Methods We have developed a method that uses realistic synthetic images of different conditions to characterize the robustness and sensitivity of CNNs in segmentation of mitochondria. Using this method, we compared performance of two widely adopted CNNs: the fully convolutional network (FCN) and the U‐Net. We further compared the two networks against the adaptive active‐mask (AAM) algorithm, a representative of high‐performance conventional segmentation algorithms.
Results The FCN and the U‐Net consistently outperformed the AAM in accuracy, robustness, and sensitivity, often by a significant margin. The U‐Net provided overall the best performance.
Conclusions Our study demonstrates superior performance of the U‐Net and the FCN in segmentation of mitochondria. It also provides quantitative measurements of the robustness and sensitivity of these networks that are essential to their applications in quantitative analysis of mitochondrial morphology.
-
This paper presents a unified framework to learn to quantify perceptual attributes (e.g., safety, attractiveness) of physical urban environments using crowd-sourced street-view photos without human annotations. The efforts of this work include two folds. First, we collect a large-scale urban image dataset in multiple major cities in U.S.A., which consists of multiple street-view photos for every place. Instead of using subjective annotations as in previous works, which are neither accurate nor consistent, we collect for every place the safety score from government’s crime event records as objective safety indicators. Second, we observe that the place-centric perception task is by nature a multi-instance regression problem since the labels are only available for places (bags), rather than images or image regions (instances). We thus introduce a deep convolutional neural network (CNN) to parameterize the instance-level scoring function, and develop an EM algorithm to alternatively estimate the primary instances (images or image regions) which affect the safety scores and train the proposed network. Our method is capable of localizing interesting images and image regions for each place.We evaluate the proposed method on a newly created dataset and a public dataset. Results with comparisons showed that our method can clearly outperform the alternative perception methods and more importantly, is capable of generating region-level safety scores to facilitate interpretations of the perception process.more » « less
-
Shape priors have been widely utilized in medical image segmentation to improve segmentation accuracy and robustness. A major way to encode such a prior shape model is to use a mesh representation, which is prone to causing self-intersection or mesh folding. Those problems require complex and expensive algorithms to mitigate. In this paper, we propose a novel shape prior directly embedded in the voxel grid space, based on gradient vector flows of a pre-segmentation. The flexible and powerful prior shape representation is ready to be extended to simultaneously segmenting multiple interacting objects with minimum separation distance constraint. The segmentation problem of multiple interacting objects with shape priors is formulated as a Markov Random Field problem, which seeks to optimize the label assignment (objects or background) for each voxel while keeping the label consistency between the neighboring voxels. The optimization problem can be efficiently solved with a single minimum s-t cut in an appropriately constructed graph. The proposed algorithm has been validated on two multi-object segmentation applications: the brain tissue segmentation in MRI images and the bladder/prostate segmentation in CT images. Both sets of experiments showed superior or competitive performance of the proposed method to the compared state-of-the-art methods.more » « less
-
Medical image analysis using deep learning has recently been prevalent, showing great performance for various downstream tasks including medical image segmentation and its sibling, volumetric image segmentation. Particularly, a typical volumetric segmentation network strongly relies on a voxel grid representation which treats volumetric data as a stack of individual voxel `slices', which allows learning to segment a voxel grid to be as straightforward as extending existing image-based segmentation networks to the 3D domain. However, using a voxel grid representation requires a large memory footprint, expensive test-time and limiting the scalability of the solutions. In this paper, we propose Point-Unet, a novel method that incorporates the eciency of deep learning with 3D point clouds into volumetric segmentation. Our key idea is to rst predict the regions of interest in the volume by learning an attentional probability map, which is then used for sampling the volume into a sparse point cloud that is subsequently segmented using a point-based neural network. We have conducted the experiments on the medical volumetric segmentation task with both a small-scale dataset Pancreas and large-scale datasets BraTS18, BraTS19, and BraTS20 challenges. A comprehensive benchmark on di erent metrics has shown that our context-aware Point-Unet robustly outperforms the SOTA voxel-based networks at both accuracies, memory usage during training, and time consumption during testing.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- The DOI is not currently available.
