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Register a new userMultiStar: Instance Segmentation of Overlapping Objects with Star-Convex Polygons
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Instance segmentation of overlapping objects in biomedical images remains a largely unsolved problem. We take up this challenge and present MultiStar, an extension to the popular instance segmentation method StarDist. The key novelty of our method is that we identify pixels at which objects overlap and use this information to improve proposal sampling and to avoid suppressing proposals of truly overlapping objects. This allows us to apply the ideas of StarDist to images with overlapping objects, while incurring only a small overhead compared to the established method. MultiStar shows promising results on two datasets and has the advantage of using a simple and easy to train network architecture.
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Hughes Perreault
, Guillaume-Alexandre Bilodeau
, Nicolas Saunier andn Maguelonne Heritier
2021
We present a novel method, called CenterPoly, for real-time instance segmentation using bounding polygons. We apply it to detect road users in dense urban environments, making it suitable for applications in intelligent transportation systems like automated vehicles. CenterPoly detects objects by their center keypoint while predicting a fixed number of polygon vertices for each object, thus performing detection and segmentation in parallel. Most of the network parameters are shared by the network heads, making it fast and lightweight enough to run at real-time speed. To properly convert mask ground-truth to polygon ground-truth, we designed a vertex selection strategy to facilitate the learning of the polygons. Additionally, to better segment overlapping objects in dense urban scenes, we also train a relative depth branch to determine which instances are closer and which are further, using available weak annotations. We propose several models with different backbones to show the possible speed / accuracy trade-offs. The models were trained and evaluated on Cityscapes, KITTI and IDD and the results are reported on their public benchmark, which are state-of-the-art at real-time speeds. Code is available at https://github.com/hu64/CenterPoly
Cell instance segmentation in Pap smear image remains challenging due to the wide existence of occlusion among translucent cytoplasm in cell clumps. Conventional methods heavily rely on accurate nuclei detection results and are easily disturbed by miscellaneous objects. In this paper, we propose a novel Instance Relation Network (IRNet) for robust overlapping cell segmentation by exploring instance relation interaction. Specifically, we propose the Instance Relation Module to construct the cell association matrix for transferring information among individual cell-instance features. With the collaboration of different instances, the augmented features gain benefits from contextual information and improve semantic consistency. Meanwhile, we proposed a sparsity constrained Duplicate Removal Module to eliminate the misalignment between classification and localization accuracy for candidates selection. The largest cervical Pap smear (CPS) dataset with more than 8000 cell annotations in Pap smear image was constructed for comprehensive evaluation. Our method outperforms other methods by a large margin, demonstrating the effectiveness of exploring instance relation.
Panoptic segmentation requires segments of both things (countable object instances) and stuff (uncountable and amorphous regions) within a single output. A common approach involves the fusion of instance segmentation (for things) and semantic segmentation (for stuff) into a non-overlapping placement of segments, and resolves overlaps. However, instance ordering with detection confidence do not correlate well with natural occlusion relationship. To resolve this issue, we propose a branch that is tasked with modeling how two instance masks should overlap one another as a binary relation. Our method, named OCFusion, is lightweight but particularly effective in the instance fusion process. OCFusion is trained with the ground truth relation derived automatically from the existing dataset annotations. We obtain state-of-the-art results on COCO and show competitive results on the Cityscapes panoptic segmentation benchmark.
We propose a simple yet effective framework for instance and panoptic segmentation, termed CondInst (conditional convolutions for instance and panoptic segmentation). In the literature, top-performing instance segmentation methods typically follow the paradigm of Mask R-CNN and rely on ROI operations (typically ROIAlign) to attend to each instance. In contrast, we propose to attend to the instances with dynamic conditional convolutions. Instead of using instance-wise ROIs as inputs to the instance mask head of fixed weights, we design dynamic instance-aware mask heads, conditioned on the instances to be predicted. CondInst enjoys three advantages: 1.) Instance and panoptic segmentation are unified into a fully convolutional network, eliminating the need for ROI cropping and feature alignment. 2.) The elimination of the ROI cropping also significantly improves the output instance mask resolution. 3.) Due to the much improved capacity of dynamically-generated conditional convolutions, the mask head can be very compact (e.g., 3 conv. layers, each having only 8 channels), leading to significantly faster inference time per instance and making the overall inference time almost constant, irrelevant to the number of instances. We demonstrate a simpler method that can achieve improved accuracy and inference speed on both instance and panoptic segmentation tasks. On the COCO dataset, we outperform a few state-of-the-art methods. We hope that CondInst can be a strong baseline for instance and panoptic segmentation. Code is available at: https://git.io/AdelaiDet
Recent advances in bioimaging have provided scientists a superior high spatial-temporal resolution to observe dynamics of living cells as 3D volumetric videos. Unfortunately, the 3D biomedical video analysis is lagging, impeded by resource insensitive human curation using off-the-shelf 3D analytic tools. Herein, biologists often need to discard a considerable amount of rich 3D spatial information by compromising on 2D analysis via maximum intensity projection. Recently, pixel embedding-based cell instance segmentation and tracking provided a neat and generalizable computing paradigm for understanding cellular dynamics. In this work, we propose a novel spatial-temporal voxel-embedding (VoxelEmbed) based learning method to perform simultaneous cell instance segmenting and tracking on 3D volumetric video sequences. Our contribution is in four-fold: (1) The proposed voxel embedding generalizes the pixel embedding with 3D context information; (2) Present a simple multi-stream learning approach that allows effective spatial-temporal embedding; (3) Accomplished an end-to-end framework for one-stage 3D cell instance segmentation and tracking without heavy parameter tuning; (4) The proposed 3D quantification is memory efficient via a single GPU with 12 GB memory. We evaluate our VoxelEmbed method on four 3D datasets (with different cell types) from the ISBI Cell Tracking Challenge. The proposed VoxelEmbed method achieved consistent superior overall performance (OP) on two densely annotated datasets. The performance is also competitive on two sparsely annotated cohorts with 20.6% and 2% of data-set having segmentation annotations. The results demonstrate that the VoxelEmbed method is a generalizable and memory-efficient solution.
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