CircleNet: Anchor-free Glomerulus Detection with Circle Representation

Nested star-shaped objects segmentation using diameter annotations

Most current deep learning based approaches for image segmentation require annotations of large datasets, which limits their application in clinical practice. We observe a mismatch between the voxelwise ground-truth that is required to optimize an objective at a voxel level and the commonly used, less time-consuming clinical annotations seeking to characterize the most important information about the patient (diameters, counts, etc.). In this study, we propose to bridge this gap for the case of multiple nested star-shaped objects (e.g., a blood vessel lumen and its outer wall) by optimizing a deep learning model based on diameter annotations. This is achieved by extracting in a differentiable manner the boundary points of the objects at training time, and by using this extraction during the backpropagation. We evaluate the proposed approach on segmentation of the carotid artery lumen and wall from multisequence MR images, thus reducing the annotation burden to only four annotated landmarks required to measure the diameters in the direction of the vessel's maximum narrowing. Our experiments show that training based on diameter annotations produces state-of-the-art weakly supervised segmentations and performs reasonably compared to full supervision. We made our code publicly available at https://gitlab.com/radiology/aim/carotid-artery-image-analysis/nested-star-shaped-objects.

Glo-In-One: holistic glomerular detection, segmentation, and lesion characterization with large-scale web image mining

Purpose: The quantitative detection, segmentation, and characterization of glomeruli from high-resolution whole slide imaging (WSI) play essential roles in the computer-assisted diagnosis and scientific research in digital renal pathology. Historically, such comprehensive quantification requires extensive programming skills to be able to handle heterogeneous and customized computational tools. To bridge the gap of performing glomerular quantification for non-technical users, we develop the Glo-In-One toolkit to achieve holistic glomerular detection, segmentation, and characterization via a single line of command. Additionally, we release a large-scale collection of 30,000 unlabeled glomerular images to further facilitate the algorithmic development of self-supervised deep learning. Approach: The inputs of the Glo-In-One toolkit are WSIs, while the outputs are (1) WSI-level multi-class circle glomerular detection results (which can be directly manipulated with ImageScope), (2) glomerular image patches with segmentation masks, and (3) different lesion types. In the current version, the fine-grained global glomerulosclerosis (GGS) characterization is provided, including assessed-solidified-GSS (associated with hypertension-related injury), disappearing-GSS (a further end result of the SGGS becoming contiguous with fibrotic interstitium), and obsolescent-GSS (nonspecific GGS increasing with aging) glomeruli. To leverage the performance of the Glo-In-One toolkit, we introduce self-supervised deep learning to glomerular quantification via large-scale web image mining. Results: The GGS fine-grained classification model achieved a decent performance compared with baseline supervised methods while only using 10% of the annotated data. The glomerular detection achieved an average precision of 0.627 with circle representations, while the glomerular segmentation achieved a 0.955 patch-wise Dice dimilarity coefficient. Conclusion: We develop and release an open-source Glo-In-One toolkit, a software with holistic glomerular detection, segmentation, and lesion characterization. This toolkit is user-friendly to non-technical users via a single line of command. The toolbox and the 30,000 web mined glomerular images have been made publicly available at https://github.com/hrlblab/Glo-In-One.

deepNIR: Datasets for Generating Synthetic NIR Images and Improved Fruit Detection System Using Deep Learning Techniques

This paper presents datasets utilised for synthetic near-infrared (NIR) image generation and bounding-box level fruit detection systems. A high-quality dataset is one of the essential building blocks that can lead to success in model generalisation and the deployment of data-driven deep neural networks. In particular, synthetic data generation tasks often require more training samples than other supervised approaches. Therefore, in this paper, we share the NIR+RGB datasets that are re-processed from two public datasets (i.e., nirscene and SEN12MS), expanded our previous study, deepFruits, and our novel NIR+RGB sweet pepper (capsicum) dataset. We oversampled from the original nirscene dataset at 10, 100, 200, and 400 ratios that yielded a total of 127 k pairs of images. From the SEN12MS satellite multispectral dataset, we selected Summer (45 k) and All seasons (180k) subsets and applied a simple yet important conversion: digital number (DN) to pixel value conversion followed by image standardisation. Our sweet pepper dataset consists of 1615 pairs of NIR+RGB images that were collected from commercial farms. We quantitatively and qualitatively demonstrate that these NIR+RGB datasets are sufficient to be used for synthetic NIR image generation. We achieved Frechet inception distances (FIDs) of 11.36, 26.53, and 40.15 for nirscene1, SEN12MS, and sweet pepper datasets, respectively. In addition, we release manual annotations of 11 fruit bounding boxes that can be exported in various formats using cloud service. Four newly added fruits (blueberry, cherry, kiwi and wheat) compound 11 novel bounding box datasets on top of our previous work presented in the deepFruits project (apple, avocado, capsicum, mango, orange, rockmelon and strawberry). The total number of bounding box instances of the dataset is 162 k and it is ready to use from a cloud service. For the evaluation of the dataset, Yolov5 single stage detector is exploited and reported impressive mean-average-precision, mAP[0.5:0.95] results of min:0.49, max:0.812. We hope these datasets are useful and serve as a baseline for future studies.

Circle Representation for Medical Object Detection

Box representation has been extensively used for object detection in computer vision. Such representation is efficacious but not necessarily optimized for biomedical objects (e.g., glomeruli), which play an essential role in renal pathology. In this paper, we propose a simple circle representation for medical object detection and introduce CircleNet, an anchor-free detection framework. Compared with the conventional bounding box representation, the proposed bounding circle representation innovates in three-fold: (1) it is optimized for ball-shaped biomedical objects; (2) The circle representation reduced the degree of freedom compared with box representation; (3) It is naturally more rotation invariant. When detecting glomeruli and nuclei on pathological images, the proposed circle representation achieved superior detection performance and be more rotation-invariant, compared with the bounding box. The code has been made publicly available: https://github.com/hrlblab/CircleNet.

A semi-supervised learning framework for micropapillary adenocarcinoma detection

PURPOSE

Micropapillary adenocarcinoma is a distinctive histological subtype of lung adenocarcinoma with poor prognosis. Computer-aided diagnosis method has the potential to provide help for its early diagnosis. But the implementation of the existing methods largely relies on massive manually labeled data and consumes a lot of time and energy. To tackle these problems, we propose a framework that applies semi-supervised learning method to detect micropapillary adenocarcinoma, which aims to utilize labeled and unlabeled data better.

METHODS

The framework consists of a teacher model and a student model. The teacher model is first obtained by using the labeled data. Then, it makes predictions on unlabeled data as pseudo-labels for students. Finally, high-quality pseudo-labels are selected and associated with the labeled data to train the student model. During the learning process of the student model, augmentation is added so that the student model generalizes better than the teacher model.

RESULTS

Experiments are conducted on our own whole slide micropapillary lung adenocarcinoma histopathology image dataset and we selected 3527 patches for the experiment. In the supervised learning, our detector achieves a precision of 0.762 and recall of 0.884. In the semi-supervised learning, our method achieves a precision of 0.775 and recall of 0.896; it is superior to other methods.

CONCLUSION

We proposed a semi-supervised learning framework for micropapillary adenocarcinoma detection, which has better performance in utilizing both labeled and unlabeled data. In addition, the detector we designed improves the detection accuracy and speed and achieves promising results in detecting micropapillary adenocarcinoma.

Holistic fine-grained global glomerulosclerosis characterization: from detection to unbalanced classification

Purpose: Recent studies have demonstrated the diagnostic and prognostic values of global glomerulosclerosis (GGS) in IgA nephropathy, aging, and end-stage renal disease. However, the fine-grained quantitative analysis of multiple GGS subtypes (e.g., obsolescent, solidified, and disappearing glomerulosclerosis) is typically a resource extensive manual process. Very few automatic methods, if any, have been developed to bridge this gap for such analytics. We present a holistic pipeline to quantify GGS (with both detection and classification) from a whole slide image in a fully automatic manner. In addition, we conduct the fine-grained classification for the subtypes of GGS. Our study releases the open-source quantitative analytical tool for fine-grained GGS characterization while tackling the technical challenges in unbalanced classification and integrating detection and classification. Approach: We present a deep learning-based framework to perform fine-grained detection and classification of GGS, with a hierarchical two-stage design. Moreover, we incorporate the state-of-the-art transfer learning techniques to achieve a more generalizable deep learning model for tackling the imbalanced distribution of our dataset. This way, we build a highly efficient WSI-to-results GGS characterization pipeline. Meanwhile, we investigated the largest fine-grained GGS cohort as of yet with 11,462 glomeruli and 10,619 nonglomeruli, which include 7841 globally sclerotic glomeruli of three distinct categories. With these data, we apply deep learning techniques to achieve (1) fine-grained GGS characterization, (2) GGS versus non-GGS classification, and (3) improved glomeruli detection results. Results: For fine-grained GGS characterization, when pretrained on the larger dataset, our model can achieve a 0.778-macro- F 1 score, compared to a 0.746-macro- F 1 score when using the regular ImageNet-pretrained weights. On the external dataset, our best model achieves an area under the curve (AUC) score of 0.994 when tasked with differentiating GGS from normal glomeruli. Using our dataset, we are able to build algorithms that allow for fine-grained classification of glomeruli lesions and are robust to distribution shifts. Conclusion: Our study showed that the proposed methods consistently improve the detection and fine-grained classification performance through both cross validation and external validation. Our code and pretrained models have been released for public use at https://github.com/luyuzhe111/glomeruli.

Map3D: Registration-Based Multi-Object Tracking on 3D Serial Whole Slide Images

There has been a long pursuit for precise and reproducible glomerular quantification on renal pathology to leverage both research and practice. When digitizing the biopsy tissue samples using whole slide imaging (WSI), a set of serial sections from the same tissue can be acquired as a stack of images, similar to frames in a video. In radiology, the stack of images (e.g., computed tomography) are naturally used to provide 3D context for organs, tissues, and tumors. In pathology, it is appealing to do a similar 3D assessment. However, the 3D identification and association of large-scale glomeruli on renal pathology is challenging due to large tissue deformation, missing tissues, and artifacts from WSI. In this paper, we propose a novel Multi-object Association for Pathology in 3D (Map3D) method for automatically identifying and associating large-scale cross-sections of 3D objects from routine serial sectioning and WSI. The innovations of the Multi-Object Association for Pathology in 3D (Map3D) method are three-fold: (1) the large-scale glomerular association is formed as a new multi-object tracking (MOT) perspective; (2) the quality-aware whole series registration is proposed to not only provide affinity estimation but also offer automatic kidney-wise quality assurance (QA) for registration; (3) a dual-path association method is proposed to tackle the large deformation, missing tissues, and artifacts during tracking. To the best of our knowledge, the Map3D method is the first approach that enables automatic and large-scale glomerular association across 3D serial sectioning using WSI. Our proposed method Map3D achieved MOTA = 44.6, which is 12.1% higher than the non-deep learning benchmarks.