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Register a new userInstance Segmentation of Biomedical Images with an Object-aware Embedding Learned with Local Constraints
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Long Chen
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Automatic instance segmentation is a problem that occurs in many biomedical applications. State-of-the-art approaches either perform semantic segmentation or refine object bounding boxes obtained from detection methods. Both suffer from crowded objects to varying degrees, merging adjacent objects or suppressing a valid object. In this work, we assign an embedding vector to each pixel through a deep neural network. The network is trained to output embedding vectors of similar directions for pixels from the same object, while adjacent objects are orthogonal in the embedding space, which effectively avoids the fusion of objects in a crowd. Our method yields state-of-the-art results even with a light-weighted backbone network on a cell segmentation (BBBC006 + DSB2018) and a leaf segmentation data set (CVPPP2017). The code and model weights are public available.
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Instance segmentation of biological images is essential for studying object behaviors and properties. The challenges, such as clustering, occlusion, and adhesion problems of the objects, make instance segmentation a non-trivial task. Current box-free instance segmentation methods typically rely on local pixel-level information. Due to a lack of global object view, these methods are prone to over- or under-segmentation. On the contrary, the box-based instance segmentation methods incorporate object detection into the segmentation, performing better in identifying the individual instances. In this paper, we propose a new box-based instance segmentation method. Mainly, we locate the object bounding boxes from their center points. The object features are subsequently reused in the segmentation branch as a guide to separate the clustered instances within an RoI patch. Along with the instance normalization, the model is able to recover the target object distribution and suppress the distribution of neighboring attached objects. Consequently, the proposed model performs excellently in segmenting the clustered objects while retaining the target object details. The proposed method achieves state-of-the-art performances on three biological datasets: cell nuclei, plant phenotyping dataset, and neural cells.
This manuscript introduces the problem of prominent object detection and recognition inspired by the fact that human seems to priorities perception of scene elements. The problem deals with finding the most important region of interest, segmenting the relevant item/object in that area, and assigning it an object class label. In other words, we are solving the three problems of saliency modeling, saliency detection, and object recognition under one umbrella. The motivation behind such a problem formulation is (1) the benefits to the knowledge representation-based vision pipelines, and (2) the potential improvements in emulating bio-inspired vision systems by solving these three problems together. We are foreseeing extending this problem formulation to fully semantically segmented scenes with instance object priority for high-level inferences in various applications including assistive vision. Along with a new problem definition, we also propose a method to achieve such a task. The proposed model predicts the most important area in the image, segments the associated objects, and labels them. The proposed problem and method are evaluated against human fixations, annotated segmentation masks, and object class categories. We define a chance level for each of the evaluation criterion to compare the proposed algorithm with. Despite the good performance of the proposed baseline, the overall evaluations indicate that the problem of prominent object detection and recognition is a challenging task that is still worth investigating further.
Multiple object tracking (MOT) is a crucial task in computer vision society. However, most tracking-by-detection MOT methods, with available detected bounding boxes, cannot effectively handle static, slow-moving and fast-moving camera scenarios simultaneously due to ego-motion and frequent occlusion. In this work, we propose a novel tracking framework, called instance-aware MOT (IA-MOT), that can track multiple objects in either static or moving cameras by jointly considering the instance-level features and object motions. First, robust appearance features are extracted from a variant of Mask R-CNN detector with an additional embedding head, by sending the given detections as the region proposals. Meanwhile, the spatial attention, which focuses on the foreground within the bounding boxes, is generated from the given instance masks and applied to the extracted embedding features. In the tracking stage, object instance masks are aligned by feature similarity and motion consistency using the Hungarian association algorithm. Moreover, object re-identification (ReID) is incorporated to recover ID switches caused by long-term occlusion or missing detection. Overall, when evaluated on the MOTS20 and KITTI-MOTS dataset, our proposed method won the first place in Track 3 of the BMTT Challenge in CVPR2020 workshops.
Although deep convolutional neural networks(CNNs) have achieved remarkable results on object detection and segmentation, pre- and post-processing steps such as region proposals and non-maximum suppression(NMS), have been required. These steps result in high computational complexity and sensitivity to hyperparameters, e.g. thresholds for NMS. In this work, we propose a novel end-to-end trainable deep neural network architecture, which consists of convolutional and recurrent layers, that generates the correct number of object instances and their bounding boxes (or segmentation masks) given an image, using only a single network evaluation without any pre- or post-processing steps. We have tested on detecting digits in multi-digit images synthesized using MNIST, automatically segmenting digits in these images, and detecting cars in the KITTI benchmark dataset. The proposed approach outperforms a strong CNN baseline on the synthesized digits datasets and shows promising results on KITTI car detection.
Accurate segmenting nuclei instances is a crucial step in computer-aided image analysis to extract rich features for cellular estimation and following diagnosis as well as treatment. While it still remains challenging because the wide existence of nuclei clusters, along with the large morphological variances among different organs make nuclei instance segmentation susceptible to over-/under-segmentation. Additionally, the inevitably subjective annotating and mislabeling prevent the network learning from reliable samples and eventually reduce the generalization capability for robustly segmenting unseen organ nuclei. To address these issues, we propose a novel deep neural network, namely Contour-aware Informative Aggregation Network (CIA-Net) with multi-level information aggregation module between two task-specific decoders. Rather than independent decoders, it leverages the merit of spatial and texture dependencies between nuclei and contour by bi-directionally aggregating task-specific features. Furthermore, we proposed a novel smooth truncated loss that modulates losses to reduce the perturbation from outliers. Consequently, the network can focus on learning from reliable and informative samples, which inherently improves the generalization capability. Experiments on the 2018 MICCAI challenge of Multi-Organ-Nuclei-Segmentation validated the effectiveness of our proposed method, surpassing all the other 35 competitive teams by a significant margin.
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