Microscopy imaging plays a vital role in understanding many biological processes in development and disease. The recent advances in automation of microscopes and development of methods and markers for live cell imaging has led to rapid growth in the amount of image data being captured. To efficiently and reliably extract useful insights from these captured sequences, automated cell tracking is essential. This is a challenging problem due to large variation in the appearance and shapes of cells depending on many factors including imaging methodology, biological characteristics of cells, cell matrix composition, labeling methodology, etc. Often cell tracking methods require a sequence-specific segmentation method and manual tuning of many tracking parameters, which limits their applicability to sequences other than those they are designed for. In this paper, we propose 1) a deep learning based cell proposal method, which proposes candidates for cells along with their scores, and 2) a cell tracking method, which links proposals in adjacent frames in a graphical model using edges representing different cellular events and poses joint cell detection and tracking as the selection of a subset of cell and edge proposals. Our method is completely automated and given enough training data can be applied to a wide variety of microscopy sequences. We evaluate our method on multiple fluorescence and phase contrast microscopy sequences containing cells of various shapes and appearances from ISBI cell tracking challenge, and show that our method outperforms existing cell tracking methods.
Code is available at: https://github.com/SaadUllahAkram/CellTracker
Xiamen University（厦门大学）；School of Information Science and Engineering, Xiamen University（厦门大学信息科学与工程学院）
Recently, some correlation filter based trackers with detection proposals have achieved state-of-the-art tracking results. However, a large number of redundant proposals given by the proposal generator may degrade the performance and speed of these trackers. In this paper, we propose an adaptive proposal selection algorithm which can generate a small number of high-quality proposals to handle the problem of scale variations for visual object tracking. Specifically, we firstly utilize the color histograms in the HSV color space to represent the instances (i.e., the initial target in the first f…
Huazhong University of Science and Technology（华中科技大学）；Horizon Robotics（地平线机器人）
Video object segmentation (VOS) aims at pixel-level object tracking given only the annotations in the first frame. Due to the large visual variations of objects in video and the lack of training samples, it remains a difficult task despite the upsurging development of deep learning. Toward solving the VOS problem, we bring in several new insights by the proposed unified framework consisting of object proposal, tracking and segmentation components. The object proposal network transfers objectness information as generic knowledge into VOS; the tracking network identifies the target object from t…
The recent trend in multiple object tracking (MOT) is heading towards leveraging deep learning to boost the tracking performance. However, it is not trivial to solve the data-association problem in an end-to-end fashion. In this paper, we propose a novel proposal-based learnable framework, which models MOT as a proposal generation, proposal scoring and trajectory inference paradigm on an affinity graph. This framework is similar to the two-stage object detector Faster RCNN, and can solve the MOT problem in a data-driven way. For proposal generation, we propose an iterative graph clustering met…
Tracking vehicles in LIDAR point clouds is a challenging task due to the sparsity of the data and the dense search space. The lack of structure in point clouds impedes the use of convolution filters usually employed in 2D object tracking. In addition, structuring point clouds is cumbersome and implies losing fine-grained information. As a result, generating proposals in 3D space is expensive and inefficient. In this paper, we leverage the dense and structured Bird Eye View (BEV) representation of LIDAR point clouds to efficiently search for objects of interest. We use an efficient Region Propo…
High quality object proposals are crucial in visual tracking algorithms that utilize region proposal network (RPN). Refinement of these proposals, typically by box regression and classification in parallel, has been popularly adopted to boost tracking performance. However, it still meets problems when dealing with complex and dynamic background. Thus motivated, in this paper we introduce an improved proposal refinement module, Cascaded Regression-Align-Classification (CRAC), which yields new state-of-the-art performances on many benchmarks. First, having observed that the offsets from box regr…
In the domain of visual tracking, most deep learning-based trackers highlight the accuracy but casting aside efficiency. Therefore, their real-world deployment on mobile platforms like the unmanned aerial vehicle (UAV) is impeded. In this work, a novel two-stage Siamese network-based method is proposed for aerial tracking, \textit{i.e.}, stage-1 for high-quality anchor proposal generation, stage-2 for refining the anchor proposal. Different from anchor-based methods with numerous pre-defined fixed-sized anchors, our no-prior method can 1) increase the robustness and generalization to different…
University of Maryland, College Park（马里兰大学帕克分校）；National Institutes of Health（美国国立卫生研究院）
The nematode Caenorhabditis elegans (C. elegans) is used as a model organism to better understand developmental biology and neurobiology. C. elegans features an invariant cell lineage, which has been catalogued and observed using fluorescence microscopy images. However, established methods to track cells in late-stage development fail to generalize once sporadic muscular twitching has begun. We build upon methodology which uses skin cells as fiducial markers to carry out cell tracking despite random twitching. In particular, we present a cell nucleus segmentation and tracking procedure which w…
Xiamen University（厦门大学）；Tsinghua University（清华大学）；Xiamen University of Technology（厦门理工学院）；Queen’s University Belfast（贝尔法斯特女王大学）
In recent years, deep learning based visual tracking methods have obtained great success owing to the powerful feature representation ability of Convolutional Neural Networks (CNNs). Among these methods, classification-based tracking methods exhibit excellent performance while their speeds are heavily limited by the expensive computation for massive proposal feature extraction. In contrast, matching-based tracking methods (such as Siamese networks) possess remarkable speed superiority. However, the absence of online updating renders these methods unadaptable to significant object appearance va…
CHOTA: A Higher Order Accuracy Metric for Cell Tracking
Institute for Information Processing – Leibniz University Hannover（汉诺威莱布尼茨大学信息处理研究所）；IT4Innovations, VSB – Technical University of Ostrava（俄斯特拉发技术大学VSB IT4Innovations研究院）
Region proposal networks (RPN) have been recently combined with the Siamese network for tracking, and shown excellent accuracy with high efficiency. Nevertheless, previously proposed one-stage Siamese-RPN trackers degenerate in presence of similar distractors and large scale variation. Addressing these issues, we propose a multi-stage tracking framework, Siamese Cascaded RPN (C-RPN), which consists of a sequence of RPNs cascaded from deep high-level to shallow low-level layers in a Siamese network. Compared to previous solutions, C-RPN has several advantages: (1) Each RPN is trained using the …
Trackastra: Transformer-based cell tracking for live-cell microscopy
Institute of Bioengineering, School of Life Sciences, EPFL（EPFL生命科学学院生物工程研究所）；Center for Scalable Data Analytics and AI (ScaDS.AI)（可扩展数据分析与人工智能中心（ScaDS.AI））；Faculty of Computer Science, TU Dresden（德累斯顿工业大学计算机科学学院）
SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter
Kanazawa University（金泽大学）；Kyushu Institute of Technology（九州工业大学）；University of Tokyo（东京大学）；Kyushu University（九州大学）；Institute of Statistical Mathematics（统计数理研究所）；JST-CREST（日本科学技术振兴机构CREST）
Oblique back-illumination capillaroscopy has recently been introduced as a method for high-quality, non-invasive blood cell imaging in human capillaries. To make this technique practical for clinical blood cell counting, solutions for automatic processing of acquired videos are needed. Here, we take the first step towards this goal, by introducing a deep learning multi-cell tracking model, named CycleTrack, which achieves accurate blood cell counting from capillaroscopic videos. CycleTrack combines two simple online tracking models, SORT and CenterTrack, and is tailored to features of capillar…
RGB-Thermal object tracking attempt to locate target object using complementary visual and thermal infrared data. Existing RGB-T trackers fuse different modalities by robust feature representation learning or adaptive modal weighting. However, how to integrate dual attention mechanism for visual tracking is still a subject that has not been studied yet. In this paper, we propose two visual attention mechanisms for robust RGB-T object tracking. Specifically, the local attention is implemented by exploiting the common visual attention of RGB and thermal data to train deep classifiers. We also in…
Kyushu University（九州大学）；The Chinese University of Hong Kong（香港中文大学）
We propose a weakly-supervised cell tracking method that can train a convolutional neural network (CNN) by using only the annotation of "cell detection" (i.e., the coordinates of cell positions) without association information, in which cell positions can be easily obtained by nuclear staining. First, we train co-detection CNN that detects cells in successive frames by using weak-labels. Our key assumption is that co-detection CNN implicitly learns association in addition to detection. To obtain the association, we propose a backward-and-forward propagation method that analyzes the corresponde…
University of Southern California（南加州大学）；Army Research Laboratory（陆军研究实验室）
Supervised and unsupervised deep trackers that rely on deep learning technologies are popular in recent years. Yet, they demand high computational complexity and a high memory cost. A green unsupervised single-object tracker, called GUSOT, that aims at object tracking for long videos under a resource-constrained environment is proposed in this work. Built upon a baseline tracker, UHP-SOT++, which works well for short-term tracking, GUSOT contains two additional new modules: 1) lost object recovery, and 2) color-saliency-based shape proposal. They help resolve the tracking loss problem and offe…
University of Houston（休斯顿大学）；Boston University（波士顿大学）；Rice University（莱斯大学）
Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new, specific cost functional. This minimization is implemented by dedicated Boltzmann machines (stochastic recurrent neural networks). Automated detection of cell divisions is handled similarly by successive minimizations of two cost functions, alternating the identification of children pairs and parent identification. We validate the proposed automatic cell trackin…
We present a novel graph neural network (GNN) approach for cell tracking in high-throughput microscopy videos. By modeling the entire time-lapse sequence as a direct graph where cell instances are represented by its nodes and their associations by its edges, we extract the entire set of cell trajectories by looking for the maximal paths in the graph. This is accomplished by several key contributions incorporated into an end-to-end deep learning framework. We exploit a deep metric learning algorithm to extract cell feature vectors that distinguish between instances of different biological cells…
Cell tracking is an essential tool in live-cell imaging to determine single-cell features, such as division patterns or elongation rates. Unlike in common multiple object tracking, in microbial live-cell experiments cells are growing, moving, and dividing over time, to form cell colonies that are densely packed in mono-layer structures. With increasing cell numbers, following the precise cell-cell associations correctly over many generations becomes more and more challenging, due to the massively increasing number of possible associations. To tackle this challenge, we propose a fast parameter-…
Online multi-object tracking (MOT) is extremely important for high-level spatial reasoning and path planning for autonomous and highly-automated vehicles. In this paper, we present a modular framework for tracking multiple objects (vehicles), capable of accepting object proposals from different sensor modalities (vision and range) and a variable number of sensors, to produce continuous object tracks. This work is a generalization of the MDP framework for MOT, with some key extensions - First, we track objects across multiple cameras and across different sensor modalities. This is done by fusin…
Conventional cell tracking methods detect multiple cells in each frame (detection) and then associate the detection results in successive time-frames (association). Most cell tracking methods perform the association task independently from the detection task. However, there is no guarantee of preserving coherence between these tasks, and lack of coherence may adversely affect tracking performance. In this paper, we propose the Motion and Position Map (MPM) that jointly represents both detection and association for not only migration but also cell division. It guarantees coherence such that if …
Harbin Institute of Technology, Shenzhen（哈尔滨工业大学（深圳））
Tracking living cells in video sequence is difficult, because of cell morphology and high similarities between cells. Tracking-by-detection methods are widely used in multi-cell tracking. We perform multi-cell tracking based on the cell centroid detection, and the performance of the detector has high impact on tracking performance. In this paper, UNet is utilized to extract inter-frame and intra-frame spatio-temporal information of cells. Detection performance of cells in mitotic phase is improved by multi-frame input. Good detection results facilitate multi-cell tracking. A mitosis detection …
This paper presents F-Siamese Tracker, a novel approach for single object tracking prominently characterized by more robustly integrating 2D and 3D information to reduce redundant search space. A main challenge in 3D single object tracking is how to reduce search space for generating appropriate 3D candidates. Instead of solely relying on 3D proposals, firstly, our method leverages the Siamese network applied on RGB images to produce 2D region proposals which are then extruded into 3D viewing frustums. Besides, we perform an online accuracy validation on the 3D frustum to generate refined poin…
PyUAT: Open-source Python framework for efficient and scalable cell tracking
Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich（于利希研究中心生物与地球科学研究所IBG-1生物技术分部）；Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University（亚琛工业大学计算系统生物技术研究所（AVT.CSB））
3D single object tracking is a key issue for autonomous following robot, where the robot should robustly track and accurately localize the target for efficient following. In this paper, we propose a 3D tracking method called 3D-SiamRPN Network to track a single target object by using raw 3D point cloud data. The proposed network consists of two subnetworks. The first subnetwork is feature embedding subnetwork which is used for point cloud feature extraction and fusion. In this subnetwork, we first use PointNet++ to extract features of point cloud from template and search branches. Then, to fus…
College of Computer Science and Technology（计算机科学与技术学院）；Zhejiang University of Technology（浙江工业大学）
By decomposing the visual tracking task into two subproblems as classification for pixel category and regression for object bounding box at this pixel, we propose a novel fully convolutional Siamese network to solve visual tracking end-to-end in a per-pixel manner. The proposed framework SiamCAR consists of two simple subnetworks: one Siamese subnetwork for feature extraction and one classification-regression subnetwork for bounding box prediction. Our framework takes ResNet-50 as backbone. Different from state-of-the-art trackers like Siamese-RPN, SiamRPN++ and SPM, which are based on region …
Hangzhou Dianzi University（杭州电子科技大学）；The University of Sydney（悉尼大学）
Current 3D single object tracking methods are typically based on VoteNet, a 3D region proposal network. Despite the success, using a single seed point feature as the cue for offset learning in VoteNet prevents high-quality 3D proposals from being generated. Moreover, seed points with different importance are treated equally in the voting process, aggravating this defect. To address these issues, we propose a novel global-local transformer voting scheme to provide more informative cues and guide the model pay more attention on potential seed points, promoting the generation of high-quality 3D p…
Tracking a target of interest in both sparse and crowded environments is a challenging problem, not yet successfully addressed in the literature. In this paper, we propose a new long-term visual tracking algorithm, learning discriminative correlation filters and using an online classifier, to track a target of interest in both sparse and crowded video sequences. First, we learn a translation correlation filter using a multi-layer hybrid of convolutional neural networks (CNN) and traditional hand-crafted features. We combine advantages of both the lower convolutional layer which retains more sp…
Multi-object tracking (MOT) in computer vision and cell tracking in biomedical image analysis are two similar research fields, whose common aim is to achieve instance level object detection/segmentation and associate such objects across different video frames. However, one major difference between these two tasks is that cell tracking also aim to detect mitosis (cell division), which is typically not considered in MOT tasks. Therefore, the acyclic oriented graphs matching (AOGM) has been used as de facto standard evaluation metrics for cell tracking, rather than directly using the evaluation m…
We present our 1st place solution to the Group Dance Multiple People Tracking Challenge. Based on MOTR: End-to-End Multiple-Object Tracking with Transformer, we explore: 1) detect queries as anchors, 2) tracking as query denoising, 3) joint training on pseudo video clips generated from CrowdHuman dataset, and 4) using the YOLOX detection proposals for the anchor initialization of detect queries. Our method achieves 73.4% HOTA on the DanceTrack test set, surpassing the second-place solution by +6.8% HOTA.
U-Net and its variants have been demonstrated to work sufficiently well in biological cell tracking and segmentation. However, these methods still suffer in the presence of complex processes such as collision of cells, mitosis and apoptosis. In this paper, we augment U-Net with Siamese matching-based tracking and propose to track individual nuclei over time. By modelling the behavioural pattern of the cells, we achieve improved segmentation and tracking performances through a re-segmentation procedure. Our preliminary investigations on the Fluo-N2DH-SIM+ and Fluo-N2DH-GOWT1 datasets demonstrat…
Cell as Point: One-Stage Framework for Efficient Cell Tracking
School of Computer Science, The University of Sydney（悉尼大学计算机科学学院）；Department of Computer Science, University of Maryland College Park（马里兰大学学院公园分校计算机科学系）；Microsoft（微软公司）
Robust Visual Tracking via Hierarchical Convolutional Features
Shanghai Jiao Tong University（上海交通大学）；Australian Centre for Robotic Vision, The University of Adelaide（阿德莱德大学澳大利亚机器人视觉中心）；Virginia Tech（弗吉尼亚理工学院暨州立大学）；University of California, Merced（加州大学默塞德分校）
Huazhong University of Science and Technology（华中科技大学）
Towards 3D object tracking in point clouds, a novel point-to-box network termed P2B is proposed in an end-to-end learning manner. Our main idea is to first localize potential target centers in 3D search area embedded with target information. Then point-driven 3D target proposal and verification are executed jointly. In this way, the time-consuming 3D exhaustive search can be avoided. Specifically, we first sample seeds from the point clouds in template and search area respectively. Then, we execute permutation-invariant feature augmentation to embed target clues from template into search area …
The University of Georgia（佐治亚大学）；University of Vermont（佛蒙特大学）
Tracking cell particles in 3D microscopy videos is a challenging task but is of great significance for modeling the motion of cells. Proper characterization of the cell's shape, evolution, and their movement over time is crucial to understanding and modeling the mechanobiology of cell migration in many diseases. One in particular, toxoplasmosis is the disease caused by the parasite Toxoplasma gondii. Roughly, one-third of the world's population tests positive for T. gondii. Its virulence is linked to its lytic cycle, predicated on its motility and ability to enter and exit nucleated cells; the…
University of Science and Technology of China（中国科学技术大学）；Hefei Comprehensive National Science Center（合肥综合性国家科学中心）
Current Siamese-based trackers mainly formulate the visual tracking into two independent subtasks, including classification and localization. They learn the classification subnetwork by processing each sample separately and neglect the relationship among positive and negative samples. Moreover, such tracking paradigm takes only the classification confidence of proposals for the final prediction, which may yield the misalignment between classification and localization. To resolve these issues, this paper proposes a ranking-based optimization algorithm to explore the relationship among different…
TransientTrack: Advanced Multi-Object Tracking and Classification of Cancer Cells with Transient Fluorescent Signals
Institute for Biomedical Informatics, Faculty of Medicine；University Hospital Cologne, University of Cologne, Cologne, Germany.；Faculty of Mathematics；Natural Sciences, University of Cologne, Cologne, Germany.；Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine；Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany；Charité Comprehensive Cancer Center, Charité Universitätsmedizin, Berlin, Germany.；Centre for Genomic Regulation, Barcelona, Spain.
Multiple object tracking (MOT) is an important technology in the field of computer vision, which is widely used in automatic driving, intelligent monitoring, behavior recognition and other directions. Among the current popular MOT methods based on deep learning, Detection Based Tracking (DBT) is the most widely used in industry, and the performance of them depend on their object detection network. At present, the DBT algorithm with good performance and the most widely used is YOLOv5-DeepSORT. Inspired by YOLOv5-DeepSORT, with the proposal of YOLOv7 network, which performs better in object dete…
Hong Kong University of Science and Technology（香港科技大学）
Self-supervised learning for visual object tracking possesses valuable advantages compared to supervised learning, such as the non-necessity of laborious human annotations and online training. In this work, we exploit an end-to-end Siamese network in a cycle-consistent self-supervised framework for object tracking. Self-supervision can be performed by taking advantage of the cycle consistency in the forward and backward tracking. To better leverage the end-to-end learning of deep networks, we propose to integrate a Siamese region proposal and mask regression network in our tracking framework s…
