Weakly Supervised Geodesic Segmentation of Egyptian Mummy CT Scans

Avik Hati, Matteo Bustreo, Diego Sona, Vittorio Murino, Alessio Del Bue

Responsive image

Auto-TLDR; A Weakly Supervised and Efficient Interactive Segmentation of Ancient Egyptian Mummies CT Scans Using Geodesic Distance Measure and GrabCut

Slides Poster

In this paper, we tackle the task of automatically analyzing 3D volumetric scans obtained from computed tomography (CT) devices. In particular, we address a particular task for which data is very limited: the segmentation of ancient Egyptian mummies CT scans. We aim at digitally unwrapping the mummy and identify different segments such as body, bandages and jewelry. The problem is complex because of the lack of annotated data for the different semantic regions to segment, thus discouraging the use of strongly supervised approaches. We, therefore, propose a weakly supervised and efficient interactive segmentation method to solve this challenging problem. After segmenting the wrapped mummy from its exterior region using histogram analysis and template matching, we first design a voxel distance measure to find an approximate solution for the body and bandage segments. Here, we use geodesic distances since voxel features as well as spatial relationship among voxels is incorporated in this measure. Next, we refine the solution using a GrabCut based segmentation together with a tracking method on the slices of the scan that assigns labels to different regions in the volume, using limited supervision in the form of scribbles drawn by the user. The efficiency of the proposed method is demonstrated using visualizations and validated through quantitative measures and qualitative unwrapping of the mummy.

Similar papers

Deep Multi-Stage Model for Automated Landmarking of Craniomaxillofacial CT Scans

Simone Palazzo, Giovanni Bellitto, Luca Prezzavento, Francesco Rundo, Ulas Bagci, Daniela Giordano, Rosalia Leonardi, Concetto Spampinato

Responsive image

Auto-TLDR; Automated Landmarking of Craniomaxillofacial CT Images Using Deep Multi-Stage Architecture

Slides Similar

In this paper we define a deep multi-stage architecture for automated landmarking of craniomaxillofacial (CMF) CT images. Our model is composed of three subnetworks that first localize, on reduced-resolution images, areas where land-marks may be found and then refine the search, at full-resolution scale, through a hierarchical structure aiming at increasing the granularity of the investigated region. The multi-stage pipeline is designed to deal with full resolution data and does not require any additional pre-processing step to reduce search space, as opposed to existing methods that can be only adopted for searching landmarks located in well-defined anatomical structures (e.g.,mandibles). The automated landmarking system is tested on identifying landmarks located in several CMF regions, achieving an average error of 0.8 mm, significantly lower than expert readings. The proposed model also outperforms baselines and is on par with existing models that employ additional upstream segmentation, on state-of-the-art benchmarks.

Segmentation of Axillary and Supraclavicular Tumoral Lymph Nodes in PET/CT: A Hybrid CNN/Component-Tree Approach

Diana Lucia Farfan Cabrera, Nicolas Gogin, David Morland, Benoît Naegel, Dimitri Papathanassiou, Nicolas Passat

Responsive image

Auto-TLDR; Coupling Convolutional Neural Networks and Component-Trees for Lymph node Segmentation from PET/CT Images

Slides Similar

The analysis of axillary and supraclavicular lymph nodes is a primary prognostic factor for the staging of breast cancer. However, due to the size of lymph nodes and the low resolution of PET data, their segmentation is challenging. We investigate the relevance of considering axillary and supraclavicular lymph node segmentation from PET/CT images by coupling Convolutional Neural Networks (CNNs) and Component-Trees (C-Trees). Building upon the U-Net architecture, we propose a framework that couples a multi-modal U-Net fed with PET and CT, coupled with a hierarchical model obtained from the PET that provides additional high-level region-based features as input channels. Our working hypotheses are twofold. First, we take advantage of both anatomical information from CT for detecting the nodes, and from functional information from PET for detecting the pathological ones. Second, we consider region-based attributes extracted from C-Tree analysis of 3D PET/CT images to improve the CNN segmentation. We carried out experiments on a dataset of 240 pathological lymph nodes from 52 patients scans, and compared our outputs with human expert-defined ground-truth, leading to promising results.

Robust Skeletonization for Plant Root Structure Reconstruction from MRI

Jannis Horn

Responsive image

Auto-TLDR; Structural reconstruction of plant roots from MRI using semantic root vs shoot segmentation and 3D skeletonization

Slides Poster Similar

Structural reconstruction of plant roots from MRI is challenging, because of low resolution and low signal-to-noise ratio of the 3D measurements which may lead to disconnectivities and wrongly connected roots. We propose a two-stage approach for this task. The first stage is based on semantic root vs. soil segmentation and finds lowest-cost paths from any root voxel to the shoot. The second stage takes the largest fully connected component generated in the first stage and uses 3D skeletonization to extract a graph structure. We evaluate our method on 22 MRI scans and compare to human expert reconstructions.

A Benchmark Dataset for Segmenting Liver, Vasculature and Lesions from Large-Scale Computed Tomography Data

Bo Wang, Zhengqing Xu, Wei Xu, Qingsen Yan, Liang Zhang, Zheng You

Responsive image

Auto-TLDR; The Biggest Treatment-Oriented Liver Cancer Dataset for Segmentation

Slides Poster Similar

How to build a high-performance liver-related computer assisted diagnosis system is an open question of great interest. However, the performance of the state-of-art algorithm is always limited by the amount of data and quality of the label. To address this problem, we propose the biggest treatment-oriented liver cancer dataset for liver surgery and treatment planning. This dataset provides 216 cases (totally about 268K frames) scanned images in contrast-enhanced computed tomography (CT). We labeled all the CT images with the liver, liver vasculature and liver tumor segmentation ground truth for train and tune segmentation algorithms in advance. Based on that, we evaluate several recent and state-of-the-art segmentation algorithms, including 7 deep learning methods, on CT sequences. All results are compared to reference segmentations five error metrics that highlight different aspects of segmentation accuracy. In general, compared with previous datasets, our dataset is really a challenging dataset. To our knowledge, the proposed dataset and benchmark allow for the first time systematic exploration of such issues, and will be made available to allow for further research in this field.

Segmentation of Intracranial Aneurysm Remnant in MRA Using Dual-Attention Atrous Net

Subhashis Banerjee, Ashis Kumar Dhara, Johan Wikström, Robin Strand

Responsive image

Auto-TLDR; Dual-Attention Atrous Net for Segmentation of Intracranial Aneurysm Remnant from MRA Images

Slides Poster Similar

Due to the advancement of non-invasive medical imaging modalities like Magnetic Resonance Angiography (MRA), an increasing number of Intracranial Aneurysm (IA) cases are being reported in recent years. The IAs are typically treated by so-called endovascular coiling, where blood flow in the IA is prevented by embolization with a platinum coil. Accurate quantification of the IA Remnant (IAR), i.e. the volume with blood flow present post treatment is the utmost important factor in choosing the right treatment planning. This is typically done by manually segmenting the aneurysm remnant from the MRA volume. Since manual segmentation of volumetric images is a labour-intensive and error-prone process, development of an automatic volumetric segmentation method is required. Segmentation of small structures such as IA, that may largely vary in size, shape, and location is considered extremely difficult. Similar intensity distribution of IAs and surrounding blood vessels makes it more challenging and susceptible to false positive. In this paper we propose a novel 3D CNN architecture called Dual-Attention Atrous Net (DAtt-ANet), which can efficiently segment IAR volumes from MRA images by reconciling features at different scales using the proposed Parallel Atrous Unit (PAU) along with the use of self-attention mechanism for extracting fine-grained features and intra-class correlation. The proposed DAtt-ANet model is trained and evaluated on a clinical MRA image dataset (prospective research project, approved by the local ethical committee) of IAR consisting of 46 subjects, annotated by an expert radiologist from our group. We compared the proposed DAtt-ANet with five state-of-the-art CNN models based on their segmentation performance. The proposed DAtt-ANet outperformed all other methods and was able to achieve a five-fold cross-validation DICE score of $0.73\pm0.06$.

Automatic Semantic Segmentation of Structural Elements related to the Spinal Cord in the Lumbar Region by Using Convolutional Neural Networks

Jhon Jairo Sáenz Gamboa, Maria De La Iglesia-Vaya, Jon Ander Gómez

Responsive image

Auto-TLDR; Semantic Segmentation of Lumbar Spine Using Convolutional Neural Networks

Slides Poster Similar

This work addresses the problem of automatically segmenting the MR images corresponding to the lumbar spine. The purpose is to detect and delimit the different structural elements like vertebrae, intervertebral discs, nerves, blood vessels, etc. This task is known as semantic segmentation. The approach proposed in this work is based on convolutional neural networks whose output is a mask where each pixel from the input image is classified into one of the possible classes. Classes were defined by radiologists and correspond to structural elements and tissues. The proposed network architectures are variants of the U-Net. Several complementary blocks were used to define the variants: spatial attention models, deep supervision and multi-kernels at input, this last block type is based on the idea of inception. Those architectures which got the best results are described in this paper, and their results are discussed. Two of the proposed architectures outperform the standard U-Net used as baseline.

A Heuristic-Based Decision Tree for Connected Components Labeling of 3D Volumes

Maximilian Söchting, Stefano Allegretti, Federico Bolelli, Costantino Grana

Responsive image

Auto-TLDR; Entropy Partitioning Decision Tree for Connected Components Labeling

Slides Poster Similar

Connected Components Labeling represents a fundamental step for many Computer Vision and Image Processing pipelines. Since the first appearance of the task in the sixties, many algorithmic solutions to optimize the computational load needed to label an image have been proposed. Among them, block-based scan approaches and decision trees revealed to be some of the most valuable strategies. However, due to the cost of the manual construction of optimal decision trees and the computational limitations of automatic strategies employed in the past, the application of blocks and decision trees has been restricted to small masks, and thus to 2D algorithms. With this paper we present a novel heuristic algorithm based on decision tree learning methodology, called Entropy Partitioning Decision Tree (EPDT). It allows to compute near-optimal decision trees for large scan masks. Experimental results demonstrate that algorithms based on the generated decision trees outperform state-of-the-art competitors.

Video Semantic Segmentation Using Deep Multi-View Representation Learning

Akrem Sellami, Salvatore Tabbone

Responsive image

Auto-TLDR; Deep Multi-view Representation Learning for Video Object Segmentation

Slides Poster Similar

In this paper, we propose a deep learning model based on deep multi-view representation learning, to address the video object segmentation task. The proposed model emphasizes the importance of the inherent correlation between video frames and incorporates a multi-view representation learning based on deep canonically correlated autoencoders. The multi-view representation learning in our model provides an efficient mechanism for capturing inherent correlations by jointly extracting useful features and learning better representation into a joint feature space, i.e., shared representation. To increase the training data and the learning capacity, we train the proposed model with pairs of video frames, i.e., $F_{a}$ and $F_{b}$. During the segmentation phase, the deep canonically correlated autoencoders model encodes useful features by processing multiple reference frames together, which is used to detect the frequently reappearing. Our model enhances the state-of-the-art deep learning-based methods that mainly focus on learning discriminative foreground representations over appearance and motion. Experimental results over two large benchmarks demonstrate the ability of the proposed method to outperform competitive approaches and to reach good performances, in terms of semantic segmentation.

One Step Clustering Based on A-Contrario Framework for Detection of Alterations in Historical Violins

Alireza Rezaei, Sylvie Le Hégarat-Mascle, Emanuel Aldea, Piercarlo Dondi, Marco Malagodi

Responsive image

Auto-TLDR; A-Contrario Clustering for the Detection of Altered Violins using UVIFL Images

Slides Poster Similar

Preventive conservation is an important practice in Cultural Heritage. The constant monitoring of the state of conservation of an artwork helps us reduce the risk of damage and number of interventions necessary. In this work, we propose a probabilistic approach for the detection of alterations on the surface of historical violins based on an a-contrario framework. Our method is a one step NFA clustering solution which considers grey-level and spatial density information in one background model. The proposed method is robust to noise and avoids parameter tuning and any assumption about the quantity of the worn out areas. We have used as input UV induced fluorescence (UVIFL) images for considering details not perceivable with visible light. Tests were conducted on image sequences included in the ``Violins UVIFL imagery'' dataset. Results illustrate the ability of the algorithm to distinguish the worn area from the surrounding regions. Comparisons with the state of the art clustering methods shows improved overall precision and recall.

Deep Recurrent-Convolutional Model for AutomatedSegmentation of Craniomaxillofacial CT Scans

Francesca Murabito, Simone Palazzo, Federica Salanitri Proietto, Francesco Rundo, Ulas Bagci, Daniela Giordano, Rosalia Leonardi, Concetto Spampinato

Responsive image

Auto-TLDR; Automated Segmentation of Anatomical Structures in Craniomaxillofacial CT Scans using Fully Convolutional Deep Networks

Slides Poster Similar

In this paper we define a deep learning architecture for automated segmentation of anatomical structures in Craniomaxillofacial (CMF) CT scans that leverages the recent success of encoder-decoder models for semantic segmentation of natural images. In particular, we propose a fully convolutional deep network that combines the advantages of recent fully convolutional models, such as Tiramisu, with squeeze-and-excitation blocks for feature recalibration, integrated with convolutional LSTMs to model spatio-temporal correlations between consecutive slices. The proposed segmentation network shows superior performance and generalization capabilities (to different structures and imaging modalities) than state of the art methods on automated segmentation of CMF structures (e.g., mandibles and airways) in several standard benchmarks (e.g., MICCAI datasets) and on new datasets proposed herein, effectively facing shape variability.

Object Segmentation Tracking from Generic Video Cues

Amirhossein Kardoost, Sabine Müller, Joachim Weickert, Margret Keuper

Responsive image

Auto-TLDR; A Light-Weight Variational Framework for Video Object Segmentation in Videos

Slides Poster Similar

We propose a light-weight variational framework for online tracking of object segmentations in videos based on optical flow and image boundaries. While high-end computer vision methods on this task rely on sequence specific training of dedicated CNN architectures, we show the potential of a variational model, based on generic video information from motion and color. Such cues are usually required for tasks such as robot navigation or grasp estimation. We leverage them directly for video object segmentation and thus provide accurate segmentations at potentially very low extra cost. Our simple method can provide competitive results compared to the costly CNN-based methods with parameter tuning. Furthermore, we show that our approach can be combined with state-of-the-art CNN-based segmentations in order to improve over their respective results. We evaluate our method on the datasets DAVIS 16,17 and SegTrack v2.

Early Wildfire Smoke Detection in Videos

Taanya Gupta, Hengyue Liu, Bir Bhanu

Responsive image

Auto-TLDR; Semi-supervised Spatio-Temporal Video Object Segmentation for Automatic Detection of Smoke in Videos during Forest Fire

Poster Similar

Recent advances in unmanned aerial vehicles and camera technology have proven useful for the detection of smoke that emerges above the trees during a forest fire. Automatic detection of smoke in videos is of great interest to Fire department. To date, in most parts of the world, the fire is not detected in its early stage and generally it turns catastrophic. This paper introduces a novel technique that integrates spatial and temporal features in a deep learning framework using semi-supervised spatio-temporal video object segmentation and dense optical flow. However, detecting this smoke in the presence of haze and without the labeled data is difficult. Considering the visibility of haze in the sky, a dark channel pre-processing method is used that reduces the amount of haze in video frames and consequently improves the detection results. Online training is performed on a video at the time of testing that reduces the need for ground-truth data. Tests using the publicly available video datasets show that the proposed algorithms outperform previous work and they are robust across different wildfire-threatened locations.

A Multi-Task Contextual Atrous Residual Network for Brain Tumor Detection & Segmentation

Ngan Le, Kashu Yamazaki, Quach Kha Gia, Thanh-Dat Truong, Marios Savvides

Responsive image

Auto-TLDR; Contextual Brain Tumor Segmentation Using 3D atrous Residual Networks and Cascaded Structures

Poster Similar

In recent years, deep neural networks have achieved state-of-the-art performance in a variety of recognition and segmentation tasks in medical imaging including brain tumor segmentation. We investigate that segmenting brain tumor is facing to the imbalanced data problem where the number of pixels belonging to background class (non tumor pixel) is much larger than the number of pixels belonging to foreground class (tumor pixel). To address this problem, we propose a multi-task network which is formed as a cascaded structure and designed to share the feature maps. Our model consists of two targets, i.e., (i) effectively differentiating brain tumor regions and (ii) estimating brain tumor masks. The first task is performed by our proposed contextual brain tumor detection network, which plays the role of an attention gate and focuses on the region around brain tumor only while ignore the background (non tumor area). Instead of processing every pixel, our contextual brain tumor detection network only processes contextual regions around ground-truth instances and this strategy helps to produce meaningful regions proposals. The second task is built upon a 3D atrous residual network and under an encode-decode network in order to effectively segment both large and small objects (brain tumor). Our 3D atrous residual network is designed with a skip connection to enables the gradient from the deep layers to be directly propagated to shallow layers, thus, features of different depths are preserved and used for refining each other. In order to incorporate larger contextual information in volume MRI data, our network is designed by 3D atrous convolution with various kernel sizes, which enlarges the receptive field of filters. Our proposed network has been evaluated on various datasets including BRATS2015, BRATS2017 and BRATS2018 datasets with both validation set and testing set. Our performance has been benchmarked by both region-based metrics and surface-based metrics. We also have conducted comparisons against state-of-the-art approaches.

Planar 3D Transfer Learning for End to End Unimodal MRI Unbalanced Data Segmentation

Martin Kolarik, Radim Burget, Carlos M. Travieso-Gonzalez, Jan Kocica

Responsive image

Auto-TLDR; Planar 3D Res-U-Net Network for Unbalanced 3D Image Segmentation using Fluid Attenuation Inversion Recover

Slides Similar

We present a novel approach of 2D to 3D transfer learning based on mapping pre-trained 2D convolutional neural network weights into planar 3D kernels. The method is validated by proposed planar 3D res-u-net network with encoder transferred from the 2D VGG-16 which is applied for a single-stage unbalanced 3D image data segmentation. In particular, we evaluate the method on the MICCAI 2016 MS lesion segmentation challenge dataset utilizing solely Fluid Attenuation Inversion Recover (FLAIR) sequence without brain extraction for training and inference to simulate real medical praxis. The planar 3D res-u-net network performed the best both in sensitivity and Dice score amongst end to end methods processing raw MRI scans and achieved comparable Dice score to a state-of-the-art unimodal not end to end approach. Complete source code was released under the open-source license and this paper is in compliance with the Machine learning Reproducibility Checklist. By implementing practical transfer learning for 3D data representation we were able to successfully segment heavily unbalanced data without selective sampling and achieved more reliable results using less training data in single modality. From medical perspective, the unimodal approach gives an advantage in real praxis as it does not require co-registration nor additional scanning time during examination. Although modern medical imaging methods capture high resolution 3D anatomy scans suitable for computer aided detection system processing, deployment of automatic systems for interpretation of radiology imaging is still rather theoretical in many medical areas. Our work aims to bridge the gap offering solution for partial research questions.

A New Geodesic-Based Feature for Characterization of 3D Shapes: Application to Soft Tissue Organ Temporal Deformations

Karim Makki, Amine Bohi, Augustin Ogier, Marc-Emmanuel Bellemare

Responsive image

Auto-TLDR; Spatio-Temporal Feature Descriptors for 3D Shape Characterization from Point Clouds

Slides Poster Similar

Spatio-temporal feature descriptors are of great importance for characterizing the local changes of 3D deformable shapes. In this study, we propose a method for characterizing 3D shapes from point clouds and we show a direct application on a study of organ temporal deformations. As an example, we characterize the behavior of the bladder during forced respiratory motion with a reduced number of 3D surface points: first, a set of equidistant points representing the vertices of quadrilateral mesh for the organ surface are tracked throughout a long dynamic MRI sequence using a large deformation diffeomorphic metric mapping (LDDMM) framework. Second, a novel 3D shape descriptor invariant to translation, scale and rotation is proposed for characterizing the temporal organ deformations by employing an Eulerian Partial Differential Equations (PDEs) methodology. We demonstrate the robustness of our feature on both synthetic 3D shapes and realistic dynamic Magnetic Resonance Imaging (MRI) data sequences portraying the bladder deformation during a forced breathing exercise. Promising results are obtained, showing that the proposed feature may be useful for several computer vision applications such as medical imaging, aerodynamics and robotics.

Motion-Supervised Co-Part Segmentation

Aliaksandr Siarohin, Subhankar Roy, Stéphane Lathuiliere, Sergey Tulyakov, Elisa Ricci, Nicu Sebe

Responsive image

Auto-TLDR; Self-supervised Co-Part Segmentation Using Motion Information from Videos

Slides Similar

Recent co-part segmentation methods mostly operate in a supervised learning setting, which requires a large amount of annotated data for training. To overcome this limitation, we propose a self-supervised deep learning method for co-part segmentation. Differently from previous works, our approach develops the idea that motion information inferred from videos can be leveraged to discover meaningful object parts. To this end, our method relies on pairs of frames sampled from the same video. The network learns to predict part segments together with a representation of the motion between two frames, which permits reconstruction of the target image. Through extensive experimental evaluation on publicly available video sequences we demonstrate that our approach can produce improved segmentation maps with respect to previous self-supervised co-part segmentation approaches.

BiLuNet: A Multi-Path Network for Semantic Segmentation on X-Ray Images

Van Luan Tran, Huei-Yung Lin, Rachel Liu, Chun-Han Tseng, Chun-Han Tseng

Responsive image

Auto-TLDR; BiLuNet: Multi-path Convolutional Neural Network for Semantic Segmentation of Lumbar vertebrae, sacrum,

Similar

Semantic segmentation and shape detection of lumbar vertebrae, sacrum, and femoral heads from clinical X-ray images are important and challenging tasks. In this paper, we propose a new multi-path convolutional neural network, BiLuNet, for semantic segmentation on X-ray images. The network is capable of medical image segmentation with very limited training data. With the shape fitting of the bones, we can identify the location of the target regions very accurately for lumbar vertebra inspection. We collected our dataset and annotated by doctors for model training and performance evaluation. Compared to the state-of-the-art methods, the proposed technique provides better mIoUs and higher success rates with the same training data. The experimental results have demonstrated the feasibility of our network to perform semantic segmentation for lumbar vertebrae, sacrum, and femoral heads.

One-Stage Multi-Task Detector for 3D Cardiac MR Imaging

Weizeng Lu, Xi Jia, Wei Chen, Nicolò Savioli, Antonio De Marvao, Linlin Shen, Declan O'Regan, Jinming Duan

Responsive image

Auto-TLDR; Multi-task Learning for Real-Time, simultaneous landmark location and bounding box detection in 3D space

Slides Poster Similar

Fast and accurate landmark location and bounding box detection are important steps in 3D medical imaging. In this paper, we propose a novel multi-task learning framework, for real-time, simultaneous landmark location and bounding box detection in 3D space. Our method extends the famous single-shot multibox detector (SSD) from single-task learning to multi-task learning and from 2D to 3D. Furthermore, we propose a post-processing approach to refine the network landmark output, by averaging the candidate landmarks. Owing to these settings, the proposed framework is fast and accurate. For 3D cardiac magnetic resonance (MR) images with size 224 × 224 × 64, our framework runs about 128 volumes per second (VPS) on GPU and achieves 6.75mm average point-to-point distance error for landmark location, which outperforms both state-of-the-art and baseline methods. We also show that segmenting the 3D image cropped with the bounding box results in both improved performance and efficiency.

Revisiting Sequence-To-Sequence Video Object Segmentation with Multi-Task Loss and Skip-Memory

Fatemeh Azimi, Benjamin Bischke, Sebastian Palacio, Federico Raue, Jörn Hees, Andreas Dengel

Responsive image

Auto-TLDR; Sequence-to-Sequence Learning for Video Object Segmentation

Slides Poster Similar

Video Object Segmentation (VOS) is an active research area of the visual domain. One of its fundamental sub-tasks is semi-supervised / one-shot learning: given only the segmentation mask for the first frame, the task is to provide pixel-accurate masks for the object over the rest of the sequence. Despite much progress in the last years, we noticed that many of the existing approaches lose objects in longer sequences, especially when the object is small or briefly occluded. In this work, we build upon a sequence-to-sequence approach that employs an encoder-decoder architecture together with a memory module for exploiting the sequential data. We further improve this approach by proposing a model that manipulates multi-scale spatio-temporal information using memory-equipped skip connections. Furthermore, we incorporate an auxiliary task based on distance classification which greatly enhances the quality of edges in segmentation masks. We compare our approach to the state of the art and show considerable improvement in the contour accuracy metric and the overall segmentation accuracy.

MTGAN: Mask and Texture-Driven Generative Adversarial Network for Lung Nodule Segmentation

Wei Chen, Qiuli Wang, Kun Wang, Dan Yang, Xiaohong Zhang, Chen Liu, Yucong Li

Responsive image

Auto-TLDR; Mask and Texture-driven Generative Adversarial Network for Lung Nodule Segmentation

Slides Poster Similar

Accurate segmentation for lung nodules in lung computed tomography (CT) scans plays a key role in the early diagnosis of lung cancer. Many existing methods, especially UNet, have made significant progress in lung nodule segmentation. However, due to the complex shapes of lung nodules and the similarity of visual characteristics between nodules and lung tissues, an accurate segmentation with few false positives of lung nodules is still a challenging problem. Considering the fact that both boundary and texture information of lung nodules are important for obtaining an accurate segmentation result, we propose a novel Mask and Texture-driven Generative Adversarial Network (MTGAN) with a joint multi-scale L1 loss for lung nodule segmentation, which takes full advantages of U-Net and adversarial training. The proposed MTGAN leverages adversarial learning strategy guided by the boundary and texture information of lung nodules to generate more accurate segmentation results with lesser false positives. We validate our model with the LIDC–IDRI dataset, and experimental results show that our method achieves excellent segmentation results for a variety of lung nodules, especially for juxtapleural nodules and low-dense nodules. Without any bells and whistles, the proposed MTGAN achieves significant segmentation performance with the Dice similarity coefficient (DSC) of 85.24% on the LIDC–IDRI dataset.

Automated Whiteboard Lecture Video Summarization by Content Region Detection and Representation

Bhargava Urala Kota, Alexander Stone, Kenny Davila, Srirangaraj Setlur, Venu Govindaraju

Responsive image

Auto-TLDR; A Framework for Summarizing Whiteboard Lecture Videos Using Feature Representations of Handwritten Content Regions

Poster Similar

Lecture videos are rapidly becoming an invaluable source of information for students across the globe. Given the large number of online courses currently available, it is important to condense the information within these videos into a compact yet representative summary that can be used for search-based applications. We propose a framework to summarize whiteboard lecture videos by finding feature representations of detected handwritten content regions to determine unique content. We investigate multi-scale histogram of gradients and embeddings from deep metric learning for feature representation. We explicitly handle occluded, growing and disappearing handwritten content. Our method is capable of producing two kinds of lecture video summaries - the unique regions themselves or so-called key content and keyframes (which contain all unique content in a video segment). We use weighted spatio-temporal conflict minimization to segment the lecture and produce keyframes from detected regions and features. We evaluate both types of summaries and find that we obtain state-of-the-art peformance in terms of number of summary keyframes while our unique content recall and precision are comparable to state-of-the-art.

Joint Supervised and Self-Supervised Learning for 3D Real World Challenges

Antonio Alliegro, Davide Boscaini, Tatiana Tommasi

Responsive image

Auto-TLDR; Self-supervision for 3D Shape Classification and Segmentation in Point Clouds

Slides Similar

Point cloud processing and 3D shape understanding are very challenging tasks for which deep learning techniques have demonstrated great potentials. Still further progresses are essential to allow artificial intelligent agents to interact with the real world. In many practical conditions the amount of annotated data may be limited and integrating new sources of knowledge becomes crucial to support autonomous learning. Here we consider several scenarios involving synthetic and real world point clouds where supervised learning fails due to data scarcity and large domain gaps. We propose to enrich standard feature representations by leveraging self-supervision through a multi-task model that can solve a 3D puzzle while learning the main task of shape classification or part segmentation. An extensive analysis investigating few-shot, transfer learning and cross-domain settings shows the effectiveness of our approach with state-of-the-art results for 3D shape classification and part segmentation.

FOANet: A Focus of Attention Network with Application to Myocardium Segmentation

Zhou Zhao, Elodie Puybareau, Nicolas Boutry, Thierry Geraud

Responsive image

Auto-TLDR; FOANet: A Hybrid Loss Function for Myocardium Segmentation of Cardiac Magnetic Resonance Images

Slides Poster Similar

In myocardium segmentation of cardiac magnetic resonance images, ambiguities often appear near the boundaries of the target domains due to tissue similarities. To address this issue, we propose a new architecture, called FOANet, which can be decomposed in three main steps: a localization step, a Gaussian-based contrast enhancement step, and a segmentation step. This architecture is supplied with a hybrid loss function that guides the FOANet to study the transformation relationship between the input image and the corresponding label in a threelevel hierarchy (pixel-, patch- and map-level), which is helpful to improve segmentation and recovery of the boundaries. We demonstrate the efficiency of our approach on two public datasets in terms of regional and boundary segmentations.

A Deep Learning Approach for the Segmentation of Myocardial Diseases

Khawala Brahim, Abdull Qayyum, Alain Lalande, Arnaud Boucher, Anis Sakly, Fabrice Meriaudeau

Responsive image

Auto-TLDR; Segmentation of Myocardium Infarction Using Late GADEMRI and SegU-Net

Slides Poster Similar

Cardiac left ventricular (LV) segmentation is of paramount essential step for both diagnosis and treatment of cardiac pathologies such as ischemia, myocardial infarction, arrhythmia and myocarditis. However, this segmentation is challenging due to high variability across patients and the potential lack of contrast between structures. In this work, we propose and evaluate a (2.5D) SegU-Net model based on the fusion of two deep learning techniques (U-Net and Seg-Net) for automated LGEMRI (Late gadolinium enhanced magnetic resonance imaging) myocardial disease (infarct core and no reflow region) quantification in a new multifield expert annotated dataset. Given that the scar tissue represents a small part of the whole MRI slices, we focused on myocardium area. Segmentation results show that this preprocessing step facilitate the learning procedure. In order to solve the class imbalance problem, we propose to apply the Jaccard loss and the Focal Loss as optimization loss function and to integrate a class weights strategy into the objective function. Late combination has been used to merge the output of the best trained models on a different set of hyperparameters. The final network segmentation performances will be useful for future comparison of new method to the current related work for this task. A total number of 2237 of slices (320 cases) were used for training/validation and 210 slices (35 cases) were used for testing. Experiments over our proposed dataset, using several evaluation metrics such Jaccard distance (IOU), Accuracy and Dice similarity coefficient (DSC), demonstrate efficiency performance in quantifying different zones of myocardium infarction across various patients. As compared to the second intra-observer study, our testing results showed that the SegUNet prediction model leads to these average dice coefficients over all segmented tissue classes, respectively : 'Background': 0.99999, 'Myocardium': 0.99434, 'Infarctus': 0.95587, 'Noreflow': 0.78187.

A Hierarchical Framework for Leaf Instance Segmentation: Application to Plant Phenotyping

Swati Bhugra, Kanish Garg, Santanu Chaudhury, Brejesh Lall

Responsive image

Auto-TLDR; Under-segmentation of plant image using a graph based formulation to extract leaf shape knowledge for the task of leaf instance segmentation

Slides Poster Similar

Image based analysis of plants is a high-throughput and non-invasive approach to study plant traits. Based on plant image data, the quantitative estimation of many plant traits (leaf area index, biomass etc.) is associated with accurate segmentation of individual leaves. However, this task is challenging due to the presence of overlapped leaves and lack of discernible boundaries between them. In addition, variability in leaf shapes and arrangement among different plant species limits the broad utilisation of current leaf instance segmentation algorithms. In this paper, we propose a novel framework that relies on under-segmentation of plant image using a graph based formulation to extract leaf shape knowledge for the task of leaf instance segmentation. These shape priors are generated based on leaf shape characteristics independent of plant species. We demonstrate the performance of the proposed framework across multiple plant dataset i.e. Arabidopsis, Komatsuna and Salad. Experimental results indicate its broad utility.

Learning to Segment Clustered Amoeboid Cells from Brightfield Microscopy Via Multi-Task Learning with Adaptive Weight Selection

Rituparna Sarkar, Suvadip Mukherjee, Elisabeth Labruyere, Jean-Christophe Olivo-Marin

Responsive image

Auto-TLDR; Supervised Cell Segmentation from Microscopy Images using Multi-task Learning in a Multi-Task Learning Paradigm

Poster Similar

Detecting and segmenting individual cells from microscopy images is critical to various life science applications. Traditional cell segmentation tools are often ill-suited for applications in brightfield microscopy due to poor contrast and intensity heterogeneity, and only a small subset are applicable to segment cells in a cluster. In this regard, we introduce a novel supervised technique for cell segmentation in a multi-task learning paradigm. A combination of a multi-task loss, based on the region and cell boundary detection, is employed for an improved prediction efficiency of the network. The learning problem is posed in a novel min-max framework which enables adaptive estimation of the hyper-parameters in an automatic fashion. The region and cell boundary predictions are combined via morphological operations and active contour model to segment individual cells. The proposed methodology is particularly suited to segment touching cells from brightfield microscopy images without manual interventions. Quantitatively, we observe an overall Dice score of 0.93 on the validation set, which is an improvement of over 15.9% on a recent unsupervised method, and outperforms the popular supervised U-net algorithm by at least 5.8% on average.

Learning Object Deformation and Motion Adaption for Semi-Supervised Video Object Segmentation

Xiaoyang Zheng, Xin Tan, Jianming Guo, Lizhuang Ma

Responsive image

Auto-TLDR; Semi-supervised Video Object Segmentation with Mask-propagation-based Model

Slides Poster Similar

We propose a novel method to solve the task of semi-supervised video object segmentation in this paper, where the mask annotation is only given at the first frame of the video sequence. A mask-propagation-based model is applied to learn the past and current information for segmentation. Besides, due to the scarcity of training data, image/mask pairs that model object deformation and shape variance are generated for the training phase. In addition, we generate the key flips between two adjacent frames for motion adaptation. The method works in an end-to-end way, without any online fine-tuning on test videos. Extensive experiments demonstrate that our method achieves competitive performance against state-of-the-art algorithms on benchmark datasets, covering cases with single object or multiple objects. We also conduct extensive ablation experiments to analyze the effectiveness of our proposed method.

Point In: Counting Trees with Weakly Supervised Segmentation Network

Pinmo Tong, Shuhui Bu, Pengcheng Han

Responsive image

Auto-TLDR; Weakly Tree counting using Deep Segmentation Network with Localization and Mask Prediction

Slides Poster Similar

For tree counting tasks, since traditional image processing methods require expensive feature engineering and are not end-to-end frameworks, this will cause additional noise and cannot be optimized overall, so this method has not been widely used in recent trends of tree counting application. Recently, many deep learning based approaches are designed for this task because of the powerful feature extracting ability. The representative way is bounding box based supervised method, but time-consuming annotations are indispensable for them. Moreover, these methods are difficult to overcome the occlusion or overlap. To solve this problem, we propose a weakly tree counting network (WTCNet) based on deep segmentation network with only point supervision. It can simultaneously complete tree counting with localization and output mask of each tree at the same time. We first adopt a novel feature extractor network (FENet) to get features of input images, and then an effective strategy is introduced to deal with different mask predictions. In the end, we propose a basic localization guidance accompany with rectification guidance to train the network. We create two different datasets and select an existing challenging plant dataset to evaluate our method on three different tasks. Experimental results show the good performance improvement of our method compared with other existing methods. Further study shows that our method has great potential to reduce human labor and provide effective ground-truth masks and the results show the superiority of our method over the advanced methods.

SynDHN: Multi-Object Fish Tracker Trained on Synthetic Underwater Videos

Mygel Andrei Martija, Prospero Naval

Responsive image

Auto-TLDR; Underwater Multi-Object Tracking in the Wild with Deep Hungarian Network

Slides Poster Similar

In this paper, we seek to extend multi-object tracking research on a relatively less explored domain, that of, underwater multi-object tracking in the wild. Multi-object fish tracking is an important task because it can provide fish monitoring systems with richer information (e.g. multiple views of the same fish) as compared to detections and it can be an invaluable input to fish behavior analysis. However, there is a lack of an annotated benchmark dataset with enough samples for this task. To circumvent the need for manual ground truth tracking annotation, we craft a synthetic dataset. Using this synthetic dataset, we train an integrated detector and tracker called SynDHN. SynDHN uses the Deep Hungarian Network (DHN), which is a differentiable approximation of the Hungarian assignment algorithm. We repurpose DHN to become the tracking component of our algorithm by performing the task of affinity estimation between detector predictions. We consider both spatial and appearance features for affinity estimation. Our results show that despite being trained on a synthetic dataset, SynDHN generalizes well to real underwater video tracking and performs better against our baseline algorithms.

A Lumen Segmentation Method in Ureteroscopy Images Based on a Deep Residual U-Net Architecture

Jorge Lazo, Marzullo Aldo, Sara Moccia, Michele Catellani, Benoit Rosa, Elena De Momi, Michel De Mathelin, Francesco Calimeri

Responsive image

Auto-TLDR; A Deep Neural Network for Ureteroscopy with Residual Units

Slides Poster Similar

Ureteroscopy is becoming the first surgical treatment option for the majority of urinary affections. This procedure is carried out using an endoscope which provides the surgeon with the visual and spatial information necessary to navigate inside the urinary tract. Having in mind the development of surgical assistance systems, that could enhance the performance of surgeon, the task of lumen segmentation is a fundamental part since this is the visual reference which marks the path that the endoscope should follow. This is something that has not been analyzed in ureteroscopy data before. However, this task presents several challenges given the image quality and the conditions itself of ureteroscopy procedures. In this paper, we study the implementation of a Deep Neural Network which exploits the advantage of residual units in an architecture based on U-Net. For the training of these networks, we analyze the use of two different color spaces: gray-scale and RGB data images. We found that training on gray-scale images gives the best results obtaining mean values of Dice Score, Precision, and Recall of 0.73, 0.58, and 0.92 respectively. The results obtained show that the use of residual U-Net could be a suitable model for further development for a computer-aided system for navigation and guidance through the urinary system.

Triplet-Path Dilated Network for Detection and Segmentation of General Pathological Images

Jiaqi Luo, Zhicheng Zhao, Fei Su, Limei Guo

Responsive image

Auto-TLDR; Triplet-path Network for One-Stage Object Detection and Segmentation in Pathological Images

Slides Similar

Deep learning has been widely applied in the field of medical image processing. However, compared with flourishing visual tasks in natural images, the progress achieved in pathological images is not remarkable, and detection and segmentation, which are among basic tasks of computer vision, are regarded as two independent tasks. In this paper, we make full use of existing datasets and construct a triplet-path network using dilated convolutions to cooperatively accomplish one-stage object detection and nuclei segmentation for general pathological images. First, in order to meet the requirement of detection and segmentation, a novel structure called triplet feature generation (TFG) is designed to extract high-resolution and multiscale features, where features from different layers can be properly integrated. Second, considering that pathological datasets are usually small, a location-aware and partially truncated loss function is proposed to improve the classification accuracy of datasets with few images and widely varying targets. We compare the performance of both object detection and instance segmentation with state-of-the-art methods. Experimental results demonstrate the effectiveness and efficiency of the proposed network on two datasets collected from multiple organs.

Vesselness Filters: A Survey with Benchmarks Applied to Liver Imaging

Jonas Lamy, Odyssée Merveille, Bertrand Kerautret, Nicolas Passat, Antoine Vacavant

Responsive image

Auto-TLDR; Comparison of Vessel Enhancement Filters for Liver Vascular Network Segmentation

Slides Poster Similar

The accurate knowledge of vascular network geometry is crucial for many clinical applications such as cardiovascular disease diagnosis and surgery planning. Vessel enhancement algorithms are often a key step to improve the robustness of vessel segmentation. A wide variety of enhancement filters exists in the literature, but they are often difficult to compare as the applications and datasets differ from a paper to another and the code is rarely available. In this article, we compare seven vessel enhancement filters covering the last twenty years literature in a unique common framework. We focus our study on the liver vascular network which is under-represented in the literature. The evaluation is made from three points of view: in the whole liver, in the vessel neighborhood and near the bifurcations. The study is performed on two publicly available datasets: the Ircad dataset (CT images) and the VascuSynth dataset adapted for MRI simulation. We discuss the strengths and weaknesses of each method in the hepatic context. In addition, the benchmark framework including a C++ implementation of each compared method is provided. An online demonstration ensures the reproducibility of the results without requiring any additional software.

Unconstrained Vision Guided UAV Based Safe Helicopter Landing

Arindam Sikdar, Abhimanyu Sahu, Debajit Sen, Rohit Mahajan, Ananda Chowdhury

Responsive image

Auto-TLDR; Autonomous Helicopter Landing in Hazardous Environments from Unmanned Aerial Images Using Constrained Graph Clustering

Slides Poster Similar

In this paper, we have addressed the problem of automated detection of safe zone(s) for helicopter landing in hazardous environments from images captured by an Unmanned Aerial Vehicle (UAV). The unconstrained motion of the image capturing drone (the UAV in our case) makes the problem further difficult. The solution pipeline consists of natural landmark detection and tracking, stereo-pair generation using constrained graph clustering, digital terrain map construction and safe landing zone detection. The main methodological contribution lies in mathematically formulating epipolar constraint and then using it in a Minimum Spanning Tree (MST) based graph clustering approach. We have also made publicly available AHL (Autonomous Helicopter Landing) dataset, a new aerial video dataset captured by a drone, with annotated ground-truths. Experimental comparisons with other competing clustering methods i) in terms of Dunn Index and Davies Bouldin Index as well as ii) for frame-level safe zone detection in terms of F-measure and confusion matrix clearly demonstrate the effectiveness of the proposed formulation.

Few Shot Learning Framework to Reduce Inter-Observer Variability in Medical Images

Sohini Roychowdhury

Responsive image

Auto-TLDR; Few-Shot Learning for Quality Image Annotation

Slides Poster Similar

Most computer aided pathology detection systems rely on large volumes of quality annotated data to aid diagnostics and follow up procedures. However, quality assuring large volumes of annotated medical image data can be subjective and expensive. In this work we present a novel standardization framework that implements three few-shot learning (FSL) models that can be iteratively trained by atmost 5 images per 3D stack to generate multiple regional proposals (RPs) per test image. These FSL models include a novel parallel echo state network framework and an augmented U-net model. Additionally, we propose a novel target label selection algorithm (TLSA) that measures relative agreeability between RPs and the manually annotated target labels to detect the ``best" quality annotation per image. Using the FSL models, our system achieves 0.28-0.64 Dice coefficient across vendor image stacks for intra-retinal cyst segmentation. Additionally, the TLSA is capable of correctly classifying high quality target labels from their noisy counterparts with 70-97% accuracy. The proposed system significantly automates high quality annotation selection on an image level while minimizing manual quality checking to 12-28% of the images only. Thus, the proposed framework is flexible to extensions for quality image annotation curation of other image stacks as well.

Motion Segmentation with Pairwise Matches and Unknown Number of Motions

Federica Arrigoni, Tomas Pajdla, Luca Magri

Responsive image

Auto-TLDR; Motion Segmentation using Multi-Modelfitting andpermutation synchronization

Slides Poster Similar

In this paper we address motion segmentation, that is the problem of clustering points in multiple images according to a number of moving objects. Two-frame correspondences are assumed as input without prior knowledge about trajectories. Our method is based on principles from ''multi-model fitting'' and ''permutation synchronization'', and - differently from previous techniques working under the same assumptions - it can handle an unknown number of motions. The proposed approach is validated on standard datasets, showing that it can correctly estimate the number of motions while maintaining comparable or better accuracy than the state of the art.

Extended Depth of Field Preserving Color Fidelity for Automated Digital Cytology

Alexandre Bouyssoux, Riadh Fezzani, Jean-Christophe Olivo-Marin

Responsive image

Auto-TLDR; Multi-Channel Extended Depth of Field for Digital cytology based on the stationary wavelet transform

Poster Similar

This paper presents a multi-channel Extended Depth of Field (EDF) method for digital cytology based on the stationary wavelet transform. With a coefficient selection rule adapted to a precise color recovery, a sharp image can be reconstructed even on images with transparent overlapping cells. The precision and the color fidelity of the proposed method is analyzed. Moreover, an experiment demonstrating the necessity of volume analysis in cytology to achieve precise segmentation on cell clumps is conducted, and the importance of color fidelity in this context is asserted. The proposed method was tested on pap-stained urothelial cells and gray-scale cervical cells with important overlapping.

Learning to Implicitly Represent 3D Human Body from Multi-Scale Features and Multi-View Images

Zhongguo Li, Magnus Oskarsson, Anders Heyden

Responsive image

Auto-TLDR; Reconstruction of 3D human bodies from multi-view images using multi-stage end-to-end neural networks

Slides Poster Similar

Reconstruction of 3D human bodies, from images, faces many challenges, due to it generally being an ill-posed problem. In this paper we present a method to reconstruct 3D human bodies from multi-view images, through learning an implicit function to represent 3D shape, based on multi-scale features extracted by multi-stage end-to-end neural networks. Our model consists of several end-to-end hourglass networks for extracting multi-scale features from multi-view images, and a fully connected network for implicit function classification from these features. Given a 3D point, it is projected to multi-view images and these images are fed into our model to extract multi-scale features. The scales of features extracted by the hourglass networks decrease with the depth of our model, which represents the information from local to global scale. Then, the multi-scale features as well as the depth of the 3D point are combined to a new feature vector and the fully connected network classifies the feature vector, in order to predict if the point lies inside or outside of the 3D mesh. The advantage of our method is that we use both local and global features in the fully connected network and represent the 3D mesh by an implicit function, which is more memory-efficient. Experiments on public datasets demonstrate that our method surpasses previous approaches in terms of the accuracy of 3D reconstruction of human bodies from images.

3D Semantic Labeling of Photogrammetry Meshes Based on Active Learning

Mengqi Rong, Shuhan Shen, Zhanyi Hu

Responsive image

Auto-TLDR; 3D Semantic Expression of Urban Scenes Based on Active Learning

Slides Poster Similar

As different urban scenes are similar but still not completely consistent, coupled with the complexity of labeling directly in 3D, high-level understanding of 3D scenes has always been a tricky problem. In this paper, we propose a procedural approach for 3D semantic expression of urban scenes based on active learning. We first start with a small labeled image set to fine-tune a semantic segmentation network and then project its probability map onto a 3D mesh model for fusion, finally outputs a 3D semantic mesh model in which each facet has a semantic label and a heat model showing each facet’s confidence. Our key observation is that our algorithm is iterative, in each iteration, we use the output semantic model as a supervision to select several valuable images for annotation to co-participate in the fine-tuning for overall improvement. In this way, we reduce the workload of labeling but not the quality of 3D semantic model. Using urban areas from two different cities, we show the potential of our method and demonstrate its effectiveness.

Neural Machine Registration for Motion Correction in Breast DCE-MRI

Federica Aprea, Stefano Marrone, Carlo Sansone

Responsive image

Auto-TLDR; A Neural Registration Network for Dynamic Contrast Enhanced-Magnetic Resonance Imaging

Slides Poster Similar

Cancer is one of the leading causes of death in the western world, with medical imaging playing a key role for early diagnosis. Focusing on breast cancer, one of the emerging imaging methodologies is Dynamic Contrast Enhanced-Magnetic Resonance Imaging (DCE-MRI). The flip side of using DCE-MRI is in its long acquisition times, often causing the patient to move, resulting in motion artefacts, namely distortions in the acquired image that can affect DCE-MRI analysis. A possible solution consists in the use of Motion Correction Techniques (MCTs), i.e. procedures intended to re-align the post-contrast image to the corresponding pre-contrast (reference) one. This task is particularly critic in DCE-MRI, due to brightness variations introduced in post-contrast images by the contrast-agent flowing. To face this problem, in this work we introduce a new MCT for breast DCE-MRI leveraging Physiologically Based PharmacoKinetic (PBPK) modelling and Artificial Neural Networks (ANN) to determine the most suitable physiologically-compliant transformation. To this aim, we propose a Neural Registration Network relying on a very task-specific loss function explicitly designed to take into account the contrast agent flowing while enforcing a correct re-alignment. We compared the obtained results against some conventional motion correction techniques, evaluating the performance on a patient-by-patient basis. Results clearly show the effectiveness of the proposed approach, resulting as the best performing even when compares against other techniques designed to take into account for brightness variations.

MedZip: 3D Medical Images Lossless Compressor Using Recurrent Neural Network (LSTM)

Omniah Nagoor, Joss Whittle, Jingjing Deng, Benjamin Mora, Mark W. Jones

Responsive image

Auto-TLDR; Recurrent Neural Network for Lossless Medical Image Compression using Long Short-Term Memory

Poster Similar

As scanners produce higher-resolution and more densely sampled images, this raises the challenge of data storage, transmission and communication within healthcare systems. Since the quality of medical images plays a crucial role in diagnosis accuracy, medical imaging compression techniques are desired to reduce scan bitrate while guaranteeing lossless reconstruction. This paper presents a lossless compression method that integrates a Recurrent Neural Network (RNN) as a 3D sequence prediction model. The aim is to learn the long dependencies of the voxel's neighbourhood in 3D using Long Short-Term Memory (LSTM) network then compress the residual error using arithmetic coding. Experiential results reveal that our method obtains a higher compression ratio achieving 15% saving compared to the state-of-the-art lossless compression standards, including JPEG-LS, JPEG2000, JP3D, HEVC, and PPMd. Our evaluation demonstrates that the proposed method generalizes well to unseen modalities CT and MRI for the lossless compression scheme. To the best of our knowledge, this is the first lossless compression method that uses LSTM neural network for 16-bit volumetric medical image compression.

BG-Net: Boundary-Guided Network for Lung Segmentation on Clinical CT Images

Rui Xu, Yi Wang, Tiantian Liu, Xinchen Ye, Lin Lin, Yen-Wei Chen, Shoji Kido, Noriyuki Tomiyama

Responsive image

Auto-TLDR; Boundary-Guided Network for Lung Segmentation on CT Images

Slides Poster Similar

Lung segmentation on CT images is a crucial step for a computer-aided diagnosis system of lung diseases. The existing deep learning based lung segmentation methods are less efficient to segment lungs on clinical CT images, especially that the segmentation on lung boundaries is not accurate enough due to complex pulmonary opacities in practical clinics. In this paper, we propose a boundary-guided network (BG-Net) to address this problem. It contains two auxiliary branches that separately segment lungs and extract the lung boundaries, and an aggregation branch that efficiently exploits lung boundary cues to guide the network for more accurate lung segmentation on clinical CT images. We evaluate the proposed method on a private dataset collected from the Osaka university hospital and four public datasets including StructSeg, HUG, VESSEL12, and a Novel Coronavirus 2019 (COVID-19) dataset. Experimental results show that the proposed method can segment lungs more accurately and outperform several other deep learning based methods.

A Transformer-Based Network for Anisotropic 3D Medical Image Segmentation

Guo Danfeng, Demetri Terzopoulos

Responsive image

Auto-TLDR; A transformer-based model to tackle the anisotropy problem in 3D medical image analysis

Slides Poster Similar

A critical challenge of applying neural networks to 3D medical image analysis is to deal with the anisotropy problem. The inter-slice contextual information contained in medical images is important, especially when the structural information of lesions is needed. However, such information often varies with cases because of variable slice spacing. Image anisotropy downgrades model performance especially when slice spacing varies significantly among training and testing datasets. ExsiWe proposed a transformer-based model to tackle the anisotropy problem. It is adaptable to different levels of anisotropy and is computationally efficient. Experiments are conducted on 3D lung cancer segmentation task. Our model achieves an average Dice score of approximately 0.87, which generally outperforms baseline models.

Enhancing Deep Semantic Segmentation of RGB-D Data with Entangled Forests

Matteo Terreran, Elia Bonetto, Stefano Ghidoni

Responsive image

Auto-TLDR; FuseNet: A Lighter Deep Learning Model for Semantic Segmentation

Slides Poster Similar

Semantic segmentation is a problem which is getting more and more attention in the computer vision community. Nowadays, deep learning methods represent the state of the art to solve this problem, and the trend is to use deeper networks to get higher performance. The drawback with such models is a higher computational cost, which makes it difficult to integrate them on mobile robot platforms. In this work we want to explore how to obtain lighter deep learning models without compromising performance. To do so we will consider the features used in the Entangled Random Forest algorithm and we will study the best strategies to integrate these within FuseNet deep network. Such new features allow us to shrink the network size without loosing performance, obtaining hence a lighter model which achieves state-of-the-art performance on the semantic segmentation task and represents an interesting alternative for mobile robotics applications, where computational power and energy are limited.

DARN: Deep Attentive Refinement Network for Liver Tumor Segmentation from 3D CT Volume

Yao Zhang, Jiang Tian, Cheng Zhong, Yang Zhang, Zhongchao Shi, Zhiqiang He

Responsive image

Auto-TLDR; Deep Attentive Refinement Network for Liver Tumor Segmentation from 3D Computed Tomography Using Multi-Level Features

Slides Poster Similar

Automatic liver tumor segmentation from 3D Computed Tomography (CT) is a necessary prerequisite in the interventions of hepatic abnormalities and surgery planning. However, accurate liver tumor segmentation remains challenging due to the large variability of tumor sizes and inhomogeneous texture. Recent advances based on Fully Convolutional Network (FCN) in liver tumor segmentation draw on success of learning discriminative multi-level features. In this paper, we propose a Deep Attentive Refinement Network (DARN) for improved liver tumor segmentation from CT volumes by fully exploiting both low and high level features embedded in different layers of FCN. Different from existing works, we exploit attention mechanism to leverage the relation of different levels of features encoded in different layers of FCN. Specifically, we introduce a Semantic Attention Refinement (SemRef) module to selectively emphasize global semantic information in low level features with the guidance of high level ones, and a Spatial Attention Refinement (SpaRef) module to adaptively enhance spatial details in high level features with the guidance of low level ones. We evaluate our network on the public MICCAI 2017 Liver Tumor Segmentation Challenge dataset (LiTS dataset) and it achieves state-of-the-art performance. The proposed refinement modules are an effective strategy to exploit multi-level features and has great potential to generalize to other medical image segmentation tasks.

From Certain to Uncertain: Toward Optimal Solution for Offline Multiple Object Tracking

Kaikai Zhao, Takashi Imaseki, Hiroshi Mouri, Einoshin Suzuki, Tetsu Matsukawa

Responsive image

Auto-TLDR; Agglomerative Hierarchical Clustering with Ensemble of Tracking Experts for Object Tracking

Slides Poster Similar

Affinity measure in object tracking outputs a similarity or distance score for given detections. As an affinity measure is typically imperfect, it generally has an uncertain region in which regarding two groups of detections as the same object or different objects based on the score can be wrong. How to reduce the uncertain region is a major challenge for most similarity-based tracking methods. Early mistakes often result in distribution drifts for tracked objects and this is another major issue for object tracking. In this paper, we propose a new offline tracking method called agglomerative hierarchical clustering with ensemble of tracking experts (AHC_ETE), to tackle the uncertain region and early mistake issues. We conduct tracking from certain to uncertain to reduce early mistakes. Meanwhile, we ensemble multiple tracking experts to reduce the uncertain region as the final one is the union of that of each tracking expert. Experiments on MOT16 datasets demonstrated the effectiveness of our method.

Superpixel-Based Refinement for Object Proposal Generation

Christian Wilms, Simone Frintrop

Responsive image

Auto-TLDR; Superpixel-based Refinement of AttentionMask for Object Segmentation

Slides Poster Similar

Precise segmentation of objects is an important problem in tasks like class-agnostic object proposal generation or instance segmentation. Deep learning-based systems usually generate segmentations of objects based on coarse feature maps, due to the inherent downsampling in CNNs. This leads to segmentation boundaries not adhering well to the object boundaries in the image. To tackle this problem, we introduce a new superpixel-based refinement approach on top of the state-of-the-art object proposal system AttentionMask. The refinement utilizes superpixel pooling for feature extraction and a novel superpixel classifier to determine if a high precision superpixel belongs to an object or not. Our experiments show an improvement of up to 26.0% in terms of average recall compared to original AttentionMask. Furthermore, qualitative and quantitative analyses of the segmentations reveal significant improvements in terms of boundary adherence for the proposed refinement compared to various deep learning-based state-of-the-art object proposal generation systems.

Weakly Supervised Body Part Segmentation with Pose Based Part Priors

Zhengyuan Yang, Yuncheng Li, Linjie Yang, Ning Zhang, Jiebo Luo

Responsive image

Auto-TLDR; Weakly Supervised Body Part Segmentation Using Weak Labels

Slides Similar

Human body part segmentation refers to the task of predicting the semantic segmentation mask for each body part. Fully supervised body part segmentation methods achieve good performances but require an enormous amount of effort to annotate part masks for training. In contrast to high annotation costs needed for a limited number of part mask annotations, a large number of weak labels such as poses and full body masks already exist and contain relevant information. Motivated by the possibility of using existing weak labels, we propose the first weakly supervised body part segmentation framework. The core idea is first converting the sparse weak labels such as keypoints to the initial estimate of body part masks, and then iteratively refine the part mask predictions. We name the initial part masks estimated from poses the "part priors". with sufficient extra weak labels, our weakly supervised framework achieves a comparable performance (62.0% mIoU) to the fully supervised method (63.6% mIoU) on the Pascal-Person-Part dataset. Furthermore, in the extended semi-supervised setting, the proposed framework outperforms the state-of-art methods. Moreover, we extend our proposed framework to other keypoint-supervised part segmentation tasks such as face parsing.

Do Not Treat Boundaries and Regions Differently: An Example on Heart Left Atrial Segmentation

Zhou Zhao, Elodie Puybareau, Nicolas Boutry, Thierry Geraud

Responsive image

Auto-TLDR; Attention Full Convolutional Network for Atrial Segmentation using ResNet-101 Architecture

Slides Similar

Atrial fibrillation is the most common heart rhythm disease. Due to a lack of understanding in matter of underlying atrial structures, current treatments are still not satisfying. Recently, with the popularity of deep learning, many segmentation methods based on fully convolutional networks have been proposed to analyze atrial structures, especially from late gadolinium-enhanced magnetic resonance imaging. However, two problems still occur: 1) segmentation results include the atrial-like background; 2) boundaries are very hard to segment. Most segmentation approaches design a specific network that mainly focuses on the regions, to the detriment of the boundaries. Therefore, this paper proposes an attention full convolutional network framework based on the ResNet-101 architecture, which focuses on boundaries as much as on regions. The additional attention module is added to have the network pay more attention on regions and then to reduce the impact of the misleading similarity of neighboring tissues. We also use a hybrid loss composed of a region loss and a boundary loss to treat boundaries and regions at the same time. We demonstrate the efficiency of the proposed approach on the MICCAI 2018 Atrial Segmentation Challenge public dataset.