Cell Segmentation and Tracking using CNN-Based Distance Predictions and a Graph-Based Matching Strategy

The accurate segmentation and tracking of cells in microscopy image sequences is an important task in biomedical research, e.g., for studying the development of tissues, organs or entire organisms. However, the segmentation of touching cells in images with a low signal-to-noise-ratio is still a challenging problem. In this paper, we present a method for the segmentation of touching cells in microscopy images. By using a novel representation of cell borders, inspired by distance maps, our method is capable to utilize not only touching cells but also close cells in the training process. Furthermore, this representation is notably robust to annotation errors and shows promising results for the segmentation of microscopy images containing in the training data underrepresented or not included cell types. For the prediction of the proposed neighbor distances, an adapted U-Net convolutional neural network (CNN) with two decoder paths is used. In addition, we adapt a graph-based cell tracking algorithm to evaluate our proposed method on the task of cell tracking. The adapted tracking algorithm includes a movement estimation in the cost function to re-link tracks with missing segmentation masks over a short sequence of frames. Our combined tracking by detection method has proven its potential in the IEEE ISBI 2020 Cell Tracking Challenge (http://celltrackingchallenge.net/) where we achieved as team KIT-Sch-GE multiple top three rankings including two top performances using a single segmentation model for the diverse data sets.Comment: 25 pages, 14 figures, methods of the team KIT-Sch-GE for the IEEE ISBI 2020 Cell Tracking Challeng

The Whole World in Your Hand: Active and Interactive Segmentation

Object segmentation is a fundamental problem in computer vision and a powerful resource for development. This paper presents three embodied approaches to the visual segmentation of objects. Each approach to segmentation is aided by the presence of a hand or arm in the proximity of the object to be segmented. The first approach is suitable for a robotic system, where the robot can use its arm to evoke object motion. The second method operates on a wearable system, viewing the world from a human's perspective, with instrumentation to help detect and segment objects that are held in the wearer's hand. The third method operates when observing a human teacher, locating periodic motion (finger/arm/object waving or tapping) and using it as a seed for segmentation. We show that object segmentation can serve as a key resource for development by demonstrating methods that exploit high-quality object segmentations to develop both low-level vision capabilities (specialized feature detectors) and high-level vision capabilities (object recognition and localization)

Unsupervised Discovery of Parts, Structure, and Dynamics

Humans easily recognize object parts and their hierarchical structure by watching how they move; they can then predict how each part moves in the future. In this paper, we propose a novel formulation that simultaneously learns a hierarchical, disentangled object representation and a dynamics model for object parts from unlabeled videos. Our Parts, Structure, and Dynamics (PSD) model learns to, first, recognize the object parts via a layered image representation; second, predict hierarchy via a structural descriptor that composes low-level concepts into a hierarchical structure; and third, model the system dynamics by predicting the future. Experiments on multiple real and synthetic datasets demonstrate that our PSD model works well on all three tasks: segmenting object parts, building their hierarchical structure, and capturing their motion distributions.Comment: ICLR 2019. The first two authors contributed equally to this wor

Deep Learning for Semantic Part Segmentation with High-Level Guidance

In this work we address the task of segmenting an object into its parts, or semantic part segmentation. We start by adapting a state-of-the-art semantic segmentation system to this task, and show that a combination of a fully-convolutional Deep CNN system coupled with Dense CRF labelling provides excellent results for a broad range of object categories. Still, this approach remains agnostic to high-level constraints between object parts. We introduce such prior information by means of the Restricted Boltzmann Machine, adapted to our task and train our model in an discriminative fashion, as a hidden CRF, demonstrating that prior information can yield additional improvements. We also investigate the performance of our approach ``in the wild'', without information concerning the objects' bounding boxes, using an object detector to guide a multi-scale segmentation scheme. We evaluate the performance of our approach on the Penn-Fudan and LFW datasets for the tasks of pedestrian parsing and face labelling respectively. We show superior performance with respect to competitive methods that have been extensively engineered on these benchmarks, as well as realistic qualitative results on part segmentation, even for occluded or deformable objects. We also provide quantitative and extensive qualitative results on three classes from the PASCAL Parts dataset. Finally, we show that our multi-scale segmentation scheme can boost accuracy, recovering segmentations for finer parts.Comment: 11 pages (including references), 3 figures, 2 table

A Multi-cut Formulation for Joint Segmentation and Tracking of Multiple Objects

Recently, Minimum Cost Multicut Formulations have been proposed and proven to be successful in both motion trajectory segmentation and multi-target tracking scenarios. Both tasks benefit from decomposing a graphical model into an optimal number of connected components based on attractive and repulsive pairwise terms. The two tasks are formulated on different levels of granularity and, accordingly, leverage mostly local information for motion segmentation and mostly high-level information for multi-target tracking. In this paper we argue that point trajectories and their local relationships can contribute to the high-level task of multi-target tracking and also argue that high-level cues from object detection and tracking are helpful to solve motion segmentation. We propose a joint graphical model for point trajectories and object detections whose Multicuts are solutions to motion segmentation {\it and} multi-target tracking problems at once. Results on the FBMS59 motion segmentation benchmark as well as on pedestrian tracking sequences from the 2D MOT 2015 benchmark demonstrate the promise of this joint approach

Human machine collaboration for foreground segmentation in images and videos

Foreground segmentation is defined as the problem of generating pixel level foreground masks for all the objects in a given image or video. Accurate foreground segmentations in images and videos have several potential applications such as improving search, training richer object detectors, image synthesis and re-targeting, scene and activity understanding, video summarization, and post-production video editing. One effective way to solve this problem is human-machine collaboration. The main idea is to let humans guide the segmentation process through some partial supervision. As humans, we are extremely good at perception and can easily identify the foreground regions. Computers, on the other hand, lack this capability, but are extremely good at continuously processing large volumes of data at the lowest level of detail with great efficiency. Bringing these complementary strengths together can lead to systems which are accurate and cost-effective at the same time. However, in any such human-machine collaboration system, cost effectiveness and higher accuracy are competing goals. While more involvement from humans can certainly lead to higher accuracy, it also leads to increased cost both in terms of time and money. On the other hand, relying more on machines is cost-effective, but algorithms are still nowhere near human-level performance. Balancing this cost versus accuracy trade-off holds the key behind success for such a hybrid system. In this thesis, I develop foreground segmentation algorithms which effectively and efficiently make use of human guidance for accurately segmenting foreground objects in images and videos. The algorithms developed in this thesis actively reason about the best modalities or interactions through which a user can provide guidance to the system for generating accurate segmentations. At the same time, these algorithms are also capable of prioritizing human guidance on instances where it is most needed. Finally, when structural similarity exists within data (e.g., adjacent frames in a video or similar images in a collection), the algorithms developed in this thesis are capable of propagating information from instances which have received human guidance to the ones which did not. Together, these characteristics result in a substantial savings in human annotation cost while generating high quality foreground segmentations in images and videos. In this thesis, I consider three categories of segmentation problems all of which can greatly benefit from human-machine collaboration. First, I consider the problem of interactive image segmentation. In traditional interactive methods a human annotator provides a coarse spatial annotation (e.g., bounding box or freehand outlines) around the object of interest to obtain a segmentation. The mode of manual annotation used affects both its accuracy and ease-of-use. Whereas existing methods assume a fixed form of input no matter the image, in this thesis I propose a data-driven algorithm which learns whether an interactive segmentation method will succeed if initialized with a given annotation mode. This allows us to predict the modality that will be sufficiently strong to yield a high quality segmentation for a given image and results in large savings in annotation costs. I also propose a novel interactive segmentation algorithm called Click Carving which can accurately segment objects in images and videos using a very simple form of human interaction---point clicks. It outperforms several state-of-the-art methods and requires only a fraction of human effort in comparison. Second, I consider the problem of segmenting images in a weakly supervised image collection. Here, we are given a collection of images all belonging to the same object category and the goal is to jointly segment the common object from all the images. For this, I develop a stagewise active approach to segmentation propagation: in each stage, the images that appear most valuable for human annotation are actively determined and labeled by human annotators, then the foreground estimates are revised in all unlabeled images accordingly. In order to identify images that, once annotated, will propagate well to other examples, I introduce an active selection procedure that operates on the joint segmentation graph over all images. It prioritizes human intervention for those images that are uncertain and influential in the graph, while also mutually diverse. Building on this, I also introduce the problem of measuring compatibility between image pairs for joint segmentation. I show that restricting the joint segmentation to only compatible image pairs results in an improved joint segmentation performance. Finally, I propose a semi-supervised approach for segmentation propagation in video. Given human supervision in some frames of a video, this information can be propagated through time. The main challenge is that the foreground object may move quickly in the scene at the same time its appearance and shape evolves over time. To address this, I propose a higher order supervoxel label consistency potential which leverages bottom-up supervoxels to enforce long-range temporal consistency during propagation. I also introduce the notion of a generic pixel-level objectness in images and videos by training a deep neural network which uses appearance and motion to automatically assign a score to each pixel capturing its likelihood to be an "object" or "background". I show that the human guidance in the semi-supervised propagation algorithm can be further augmented with the generic pixel-objectness scores to obtain an even more accurate foreground segmentation in videos. Throughout, I provide extensive evaluation on challenging datasets and also compare with many state-of-the-art methods and other baselines validating the strengths of proposed algorithms. The outcomes across several different experiments show that the proposed human-machine collaboration algorithms achieve accurate segmentation of foreground objects in images and videos while saving a large amount of human annotation effort.Computer Science