ASIST: Annotation-free synthetic instance segmentation and tracking by adversarial simulations. (July 2021)

• Record Type: Journal Article
• Authors: Liu, Quan; Gaeta, Isabella M.; Zhao, Mengyang; Deng, Ruining; Jha, Aadarsh; Millis, Bryan A.; Mahadevan-Jansen, Anita; Tyska, Matthew J.; Huo, Yuankai
• Is Part Of: Computers in biology and medicine. Volume 134(2021)
• Publication Date: 2021-07
• Subjects: Annotation free -- Segmentation -- Tracking -- Cellular -- Subcelluar; Medicine -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; 610.285
• DOI: 10.1016/j.compbiomed.2021.104501
• Languages: English
• ISSNs: 0010-4825

Abstract

Abstract: Background: The quantitative analysis of microscope videos often requires instance segmentation and tracking of cellular and subcellular objects. The traditional method consists of two stages: (1) performing instance object segmentation of each frame, and (2) associating objects frame-by-frame. Recently, pixel-embedding-based deep learning approaches these two steps simultaneously as a single stage holistic solution. Pixel-embedding-based learning forces similar feature representation of pixels from the same object, while maximizing the difference of feature representations from different objects. However, such deep learning methods require consistent annotations not only spatially (for segmentation), but also temporally (for tracking). In computer vision, annotated training data with consistent segmentation and tracking is resource intensive, the severity of which is multiplied in microscopy imaging due to (1) dense objects (e.g., overlapping or touching), and (2) high dynamics (e.g., irregular motion and mitosis). Adversarial simulations have provided successful solutions to alleviate the lack of such annotations in dynamics scenes in computer vision, such as using simulated environments (e.g., computer games) to train real-world self-driving systems. Methods: In this paper, we propose an annotation-free synthetic instance segmentation and tracking (ASIST) method with adversarial simulation and single-stage pixel-embedding based learning. Contribution: The contribution of this paper is three-fold: (1) the proposed method aggregates adversarial simulations and single-stage pixel-embedding based deep learning (2) the method is assessed with both the cellular (i.e., HeLa cells); and subcellular (i.e., microvilli) objects; and (3) to the best of our knowledge, this is the first study to explore annotation-free instance segmentation and tracking study for microscope videos. Results: The ASIST method achieved an important step forward, when compared with fully supervised approaches: ASIST shows 7%–11% higher segmentation, detection and tracking performance on microvilli relative to fully supervised methods, and comparable performance on Hela cell videos. Highlights: Aggregating adversarial simulations and single-stage pixel embedding based learning. Simulate shape variations of cellular objects, with circles as a middle representation. Annotation-free pixel embedding based cell instance segmentation and tracking. Assessed with both the cellular and subcellular objects.