Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userLearning Metric Graphs for Neuron Segmentation In Electron Microscopy Images
253
0
0.0
(
0
)
Added by
Kyle Luther
Publication date
2019
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
In the deep metric learning approach to image segmentation, a convolutional net densely generates feature vectors at the pixels of an image. Pairs of feature vectors are trained to be similar or different, depending on whether the corresponding pixels belong to same or different ground truth segments. To segment a new image, the feature vectors are computed and clustered. Both empirically and theoretically, it is unclear whether or when deep metric learning is superior to the more conventional approach of directly predicting an affinity graph with a convolutional net. We compare the two approaches using brain images from serial section electron microscopy images, which constitute an especially challenging example of instance segmentation. We first show that seed-based postprocessing of the feature vectors, as originally proposed, produces inferior accuracy because it is difficult for the convolutional net to predict feature vectors that remain uniform across large objects. Then we consider postprocessing by thresholding a nearest neighbor graph followed by connected components. In this case, segmentations from a metric graph turn out to be competitive or even superior to segmentations from a directly predicted affinity graph. To explain these findings theoretically, we invoke the property that the metric function satisfies the triangle inequality. Then we show with an example where this constraint suppresses noise, causing connected components to more robustly segment a metric graph than an unconstrained affinity graph.
rate research
Read More
Morphology based analysis of cell types has been an area of great interest to the neuroscience community for several decades. Recently, high resolution electron microscopy (EM) datasets of the mouse brain have opened up opportunities for data analysis at a level of detail that was previously impossible. These datasets are very large in nature and thus, manual analysis is not a practical solution. Of particular interest are details to the level of post synaptic structures. This paper proposes a fully automated framework for analysis of post-synaptic structure based neuron analysis from EM data. The processing framework involves shape extraction, representation with an autoencoder, and whole cell modeling and analysis based on shape distributions. We apply our novel framework on a dataset of 1031 neurons obtained from imaging a 1mm x 1mm x 40 micrometer volume of the mouse visual cortex and show the strength of our method in clustering and classification of neuronal shapes.
Electron microscopy is widely used to explore defects in crystal structures, but human detecting of defects is often time-consuming, error-prone, and unreliable, and is not scalable to large numbers of images or real-time analysis. In this work, we discuss the application of machine learning approaches to find the location and geometry of different defect clusters in irradiated steels. We show that a deep learning based Faster R-CNN analysis system has a performance comparable to human analysis with relatively small training data sets. This study proves the promising ability to apply deep learning to assist the development of automated microscopy data analysis even when multiple features are present and paves the way for fast, scalable, and reliable analysis systems for massive amounts of modern electron microscopy data.
We propose a new method for semantic instance segmentation, by first computing how likely two pixels are to belong to the same object, and then by grouping similar pixels together. Our similarity metric is based on a deep, fully convolutional embedding model. Our grouping method is based on selecting all points that are sufficiently similar to a set of seed points, chosen from a deep, fully convolutional scoring model. We show competitive results on the Pascal VOC instance segmentation benchmark.
Deep Metric Learning (DML) is helpful in computer vision tasks. In this paper, we firstly introduce DML into image co-segmentation. We propose a novel Triplet loss for Image Segmentation, called IS-Triplet loss for short, and combine it with traditional image segmentation loss. Different from the general DML task which learns the metric between pictures, we treat each pixel as a sample, and use their embedded features in high-dimensional space to form triples, then we tend to force the distance between pixels of different categories greater than of the same category by optimizing IS-Triplet loss so that the pixels from different categories are easier to be distinguished in the high-dimensional feature space. We further present an efficient triple sampling strategy to make a feasible computation of IS-Triplet loss. Finally, the IS-Triplet loss is combined with 3 traditional image segmentation losses to perform image segmentation. We apply the proposed approach to image co-segmentation and test it on the SBCoseg dataset and the Internet dataset. The experimental result shows that our approach can effectively improve the discrimination of pixels categories in high-dimensional space and thus help traditional loss achieve better performance of image segmentation with fewer training epochs.
Semantic segmentation is a crucial step in many Earth observation tasks. Large quantity of pixel-level annotation is required to train deep networks for semantic segmentation. Earth observation techniques are applied to varieties of applications and since classes vary widely depending on the applications, therefore, domain knowledge is often required to label Earth observation images, impeding availability of labeled training data in many Earth observation applications. To tackle these challenges, in this paper we propose an unsupervised semantic segmentation method that can be trained using just a single unlabeled scene. Remote sensing scenes are generally large. The proposed method exploits this property to sample smaller patches from the larger scene and uses deep clustering and contrastive learning to refine the weights of a lightweight deep model composed of a series of the convolution layers along with an embedded channel attention. After unsupervised training on the target image/scene, the model automatically segregates the major classes present in the scene and produces the segmentation map. Experimental results on the Vaihingen dataset demonstrate the efficacy of the proposed method.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
