Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images.

BACKGROUND AND OBJECTIVE: Cell segmentation in bright-field histological slides is a crucial topic in medical image analysis. Having access to accurate segmentation allows researchers to examine the relationship between cellular morphology and clinical observations. Unfortunately, most segmentation methods known today are limited to nuclei and cannot segment the cytoplasm. METHODS: We present a new network architecture Cyto R-CNN that is able to accurately segment whole cells (with both the nucleus and the cytoplasm) in bright-field images. We also present a new dataset CytoNuke, consisting of multiple thousand manual annotations of head and neck squamous cell carcinoma cells. Utilizing this dataset, we compared the performance of Cyto R-CNN to other popular cell segmentation algorithms, including QuPath's built-in algorithm, StarDist, Cellpose and a multi-scale Attention Deeplabv3+. To evaluate segmentation performance, we calculated AP50, AP75 and measured 17 morphological and staining-related features for all detected cells. We compared these measurements to the gold standard of manual segmentation using the Kolmogorov-Smirnov test. RESULTS: Cyto R-CNN achieved an AP50 of 58.65% and an AP75 of 11.56% in whole-cell segmentation, outperforming all other methods (QuPath 19.46/0.91%; StarDist 45.33/2.32%; Cellpose 31.85/5.61%, Deeplabv3+ 3.97/1.01%). Cell features derived from Cyto R-CNN showed the best agreement to the gold standard (D¯=0.15) outperforming QuPath (D¯=0.22), StarDist (D¯=0.25), Cellpose (D¯=0.23) and Deeplabv3+ (D¯=0.33). CONCLUSION: Our newly proposed Cyto R-CNN architecture outperforms current algorithms in whole-cell segmentation while providing more reliable cell measurements than any other model. This could improve digital pathology workflows, potentially leading to improved diagnosis. Moreover, our published dataset can be used to develop further models in the future.

HOTA: A Higher Order Metric for Evaluating Multi-object Tracking.

Multi-object tracking (MOT) has been notoriously difficult to evaluate. Previous metrics overemphasize the importance of either detection or association. To address this, we present a novel MOT evaluation metric, higher order tracking accuracy (HOTA), which explicitly balances the effect of performing accurate detection, association and localization into a single unified metric for comparing trackers. HOTA decomposes into a family of sub-metrics which are able to evaluate each of five basic error types separately, which enables clear analysis of tracking performance. We evaluate the effectiveness of HOTA on the MOTChallenge benchmark, and show that it is able to capture important aspects of MOT performance not previously taken into account by established metrics. Furthermore, we show HOTA scores better align with human visual evaluation of tracking performance.

Efficient & Effective Prioritized Matching for Large-Scale Image-Based Localization.

Accurately determining the position and orientation from which an image was taken, i.e., computing the camera pose, is a fundamental step in many Computer Vision applications. The pose can be recovered from 2D-3D matches between 2D image positions and points in a 3D model of the scene. Recent advances in Structure-from-Motion allow us to reconstruct large scenes and thus create the need for image-based localization methods that efficiently handle large-scale 3D models while still being effective, i.e., while localizing as many images as possible. This paper presents an approach for large scale image-based localization that is both efficient and effective. At the core of our approach is a novel prioritized matching step that enables us to first consider features more likely to yield 2D-to-3D matches and to terminate the correspondence search as soon as enough matches have been found. Matches initially lost due to quantization are efficiently recovered by integrating 3D-to-2D search. We show how visibility information from the reconstruction process can be used to improve the efficiency of our approach. We evaluate the performance of our method through extensive experiments and demonstrate that it offers the best combination of efficiency and effectiveness among current state-of-the-art approaches for localization.

Online Multiperson Tracking-by-Detection from a Single, Uncalibrated Camera.

In this paper, we address the problem of automatically detecting and tracking a variable number of persons in complex scenes using a monocular, potentially moving, uncalibrated camera. We propose a novel approach for multiperson tracking-by-detection in a particle filtering framework. In addition to final high-confidence detections, our algorithm uses the continuous confidence of pedestrian detectors and online-trained, instance-specific classifiers as a graded observation model. Thus, generic object category knowledge is complemented by instance-specific information. The main contribution of this paper is to explore how these unreliable information sources can be used for robust multiperson tracking. The algorithm detects and tracks a large number of dynamically moving people in complex scenes with occlusions, does not rely on background modeling, requires no camera or ground plane calibration, and only makes use of information from the past. Hence, it imposes very few restrictions and is suitable for online applications. Our experiments show that the method yields good tracking performance in a large variety of highly dynamic scenarios, such as typical surveillance videos, webcam footage, or sports sequences. We demonstrate that our algorithm outperforms other methods that rely on additional information. Furthermore, we analyze the influence of different algorithm components on the robustness.

Robust multiperson tracking from a mobile platform.

In this paper, we address the problem of multiperson tracking in busy pedestrian zones using a stereo rig mounted on a mobile platform. The complexity of the problem calls for an integrated solution that extracts as much visual information as possible and combines it through cognitive feedback cycles. We propose such an approach, which jointly estimates camera position, stereo depth, object detection, and tracking. The interplay between those components is represented by a graphical model. Since the model has to incorporate object-object interactions and temporal links to past frames, direct inference is intractable. We, therefore, propose a two-stage procedure: for each frame, we first solve a simplified version of the model (disregarding interactions and temporal continuity) to estimate the scene geometry and an overcomplete set of object detections. Conditioned on these results, we then address object interactions, tracking, and prediction in a second step. The approach is experimentally evaluated on several long and difficult video sequences from busy inner-city locations. Our results show that the proposed integration makes it possible to deliver robust tracking performance in scenes of realistic complexity.

Coupled object detection and tracking from static cameras and moving vehicles.

We present a novel approach for multi-object tracking which considers object detection and spacetime trajectory estimation as a coupled optimization problem. Our approach is formulated in a Minimum Description Length hypothesis selection framework, which allows it to recover from mismatches and temporarily lost tracks. Building upon a state-of-the-art object detector, it performs multiview/multicategory object recognition to detect cars and pedestrians in the input images. The 2D object detections are checked for their consistency with (automatically estimated) scene geometry and are converted to 3D observations which are accumulated in a world coordinate frame. A subsequent trajectory estimation module analyzes the resulting 3D observations to find phyically plausible spacetime trajectories. Tracking is achieved by performing model selection after every frame. At each time instant, our approach searches for the globally optimal set of spacetime trajectories which provides the best explanation for the current image and for all evidence collected so far, while satisfying the constraints that no two objects may occupy the same physical space, nor explain the same image pixels at any point in time. Successful trajectory hypotheses are then fed back to guide object detection in future frames. The optimization procedure is kept efficient throught incremental computation and conservative hypothesis pruning. We evaluate our approach on several challenging video sequences and demonstrate its performance on both a surveillance-type scenario and a scenario where the input videos are taken from inside a moving vehicle passing through crowded city areas.