arXiv subjects

Won-Ki Jeong

Publications and source records attributed to Won-Ki Jeong.

29 records · Page 2Linked to original sources

arXiv2023

DiffMix: Diffusion Model-based Data Synthesis for Nuclei Segmentation and Classification in Imbalanced Pathology Image Datasets

Nuclei segmentation and classification is a significant process in pathology image analysis. Deep learning-based approaches have greatly contributed to the higher accuracy of this task. However, those approaches suffer from the imbalanced nuclei data composition, which shows lower classification performance on the rare nuclei class. In this paper, we propose a realistic data synthesis method using a diffusion model. We generate two types of virtual patches to enlarge the training data distribution, which is for balancing the nuclei class variance and for enlarging the chance to look at various nuclei. After that, we use a semantic-label-conditioned diffusion model to generate realistic and high-quality image samples. We demonstrate the efficacy of our method by experiment results on two imbalanced nuclei datasets, improving the state-of-the-art networks. The experimental results suggest that the proposed method improves the classification performance of the rare type nuclei classification, while showing superior segmentation and classification performance in imbalanced pathology nuclei datasets.

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arXiv2023

Scribble-supervised Cell Segmentation Using Multiscale Contrastive Regularization

Current state-of-the-art supervised deep learning-based segmentation approaches have demonstrated superior performance in medical image segmentation tasks. However, such supervised approaches require fully annotated pixel-level ground-truth labels, which are labor-intensive and time-consuming to acquire. Recently, Scribble2Label (S2L) demonstrated that using only a handful of scribbles with self-supervised learning can generate accurate segmentation results without full annotation. However, owing to the relatively small size of scribbles, the model is prone to overfit and the results may be biased to the selection of scribbles. In this work, we address this issue by employing a novel multiscale contrastive regularization term for S2L. The main idea is to extract features from intermediate layers of the neural network for contrastive loss so that structures at various scales can be effectively separated. To verify the efficacy of our method, we conducted ablation studies on well-known datasets, such as Data Science Bowl 2018 and MoNuSeg. The results show that the proposed multiscale contrastive loss is effective in improving the performance of S2L, which is comparable to that of the supervised learning segmentation method.

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arXiv2023

I2V: Towards Texture-Aware Self-Supervised Blind Denoising using Self-Residual Learning for Real-World Images

Although the advances of self-supervised blind denoising are significantly superior to conventional approaches without clean supervision in synthetic noise scenarios, it shows poor quality in real-world images due to spatially correlated noise corruption. Recently, pixel-shuffle downsampling (PD) has been proposed to eliminate the spatial correlation of noise. A study combining a blind spot network (BSN) and asymmetric PD (AP) successfully demonstrated that self-supervised blind denoising is applicable to real-world noisy images. However, PD-based inference may degrade texture details in the testing phase because high-frequency details (e.g., edges) are destroyed in the downsampled images. To avoid such an issue, we propose self-residual learning without the PD process to maintain texture information. We also propose an order-variant PD constraint, noise prior loss, and an efficient inference scheme (progressive random-replacing refinement ($\text{PR}^3$)) to boost overall performance. The results of extensive experiments show that the proposed method outperforms state-of-the-art self-supervised blind denoising approaches, including several supervised learning methods, in terms of PSNR, SSIM, LPIPS, and DISTS in real-world sRGB images.

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arXiv2021

ISCL: Interdependent Self-Cooperative Learning for Unpaired Image Denoising

With the advent of advances in self-supervised learning, paired clean-noisy data are no longer required in deep learning-based image denoising. However, existing blind denoising methods still require the assumption with regard to noise characteristics, such as zero-mean noise distribution and pixel-wise noise-signal independence; this hinders wide adaptation of the method in the medical domain. On the other hand, unpaired learning can overcome limitations related to the assumption on noise characteristics, which makes it more feasible for collecting the training data in real-world scenarios. In this paper, we propose a novel image denoising scheme, Interdependent Self-Cooperative Learning (ISCL), that leverages unpaired learning by combining cyclic adversarial learning with self-supervised residual learning. Unlike the existing unpaired image denoising methods relying on matching data distributions in different domains, the two architectures in ISCL, designed for different tasks, complement each other and boost the learning process. To assess the performance of the proposed method, we conducted extensive experiments in various biomedical image degradation scenarios, such as noise caused by physical characteristics of electron microscopy (EM) devices (film and charging noise), and structural noise found in low-dose computer tomography (CT). We demonstrate that the image quality of our method is superior to conventional and current state-of-the-art deep learning-based image denoising methods, including supervised learning.

cs.CV↗

arXiv2021

MitoVis: A Visually-guided Interactive Intelligent System for Neuronal Mitochondria Analysis

Neurons have a polarized structure, including dendrites and axons, and compartment-specific functions can be affected by dwelling mitochondria. It is known that the morphology of mitochondria is closely related to the functions of neurons and neurodegenerative diseases. Even though several deep learning methods have been developed to automatically analyze the morphology of mitochondria, the application of existing methods to actual analysis still encounters several difficulties. Since the performance of pre-trained deep learning model may vary depending on the target data, re-training of the model is often required. Besides, even though deep learning has shown superior performance under a constrained setup, there are always errors that need to be corrected by humans in real analysis. To address these issues, we introduce MitoVis, a novel visualization system for end-to-end data processing and interactive analysis of the morphology of neuronal mitochondria. MitoVis enables interactive fine-tuning of a pre-trained neural network model without the domain knowledge of machine learning, which allows neuroscientists to easily leverage deep learning in their research. MitoVis also provides novel visual guides and interactive proofreading functions so that the users can quickly identify and correct errors in the result with minimal effort. We demonstrate the usefulness and efficacy of the system via a case study conducted by a neuroscientist on a real analysis scenario. The result shows that MitoVis allows up to 15x faster analysis with similar accuracy compared to the fully manual analysis method.

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arXiv2020

Noise2Kernel: Adaptive Self-Supervised Blind Denoising using a Dilated Convolutional Kernel Architecture

With the advent of recent advances in unsupervised learning, efficient training of a deep network for image denoising without pairs of noisy and clean images has become feasible. However, most current unsupervised denoising methods are built on the assumption of zero-mean noise under the signal-independent condition. This assumption causes blind denoising techniques to suffer brightness shifting problems on images that are greatly corrupted by extreme noise such as salt-and-pepper noise. Moreover, most blind denoising methods require a random masking scheme for training to ensure the invariance of the denoising process. In this paper, we propose a dilated convolutional network that satisfies an invariant property, allowing efficient kernel-based training without random masking. We also propose an adaptive self-supervision loss to circumvent the requirement of zero-mean constraint, which is specifically effective in removing salt-and-pepper or hybrid noise where a prior knowledge of noise statistics is not readily available. We demonstrate the efficacy of the proposed method by comparing it with state-of-the-art denoising methods using various examples.

eess.IV↗

arXiv2020

Scribble2Label: Scribble-Supervised Cell Segmentation via Self-Generating Pseudo-Labels with Consistency

Segmentation is a fundamental process in microscopic cell image analysis. With the advent of recent advances in deep learning, more accurate and high-throughput cell segmentation has become feasible. However, most existing deep learning-based cell segmentation algorithms require fully annotated ground-truth cell labels, which are time-consuming and labor-intensive to generate. In this paper, we introduce Scribble2Label, a novel weakly-supervised cell segmentation framework that exploits only a handful of scribble annotations without full segmentation labels. The core idea is to combine pseudo-labeling and label filtering to generate reliable labels from weak supervision. For this, we leverage the consistency of predictions by iteratively averaging the predictions to improve pseudo labels. We demonstrate the performance of Scribble2Label by comparing it to several state-of-the-art cell segmentation methods with various cell image modalities, including bright-field, fluorescence, and electron microscopy. We also show that our method performs robustly across different levels of scribble details, which confirms that only a few scribble annotations are required in real-use cases.

cs.CV↗

arXiv2020

Reinforced Coloring for End-to-End Instance Segmentation

Instance segmentation is one of the actively studied research topics in computer vision in which many objects of interest should be separated individually. While many feed-forward networks produce high-quality segmentation on different types of images, their results often suffer from topological errors (merging or splitting) for segmentation of many objects, requiring post-processing. Existing iterative methods, on the other hand, extract a single object at a time using discriminative knowledge-based properties (shapes, boundaries, etc.) without relying on post-processing, but they do not scale well. To exploit the advantages of conventional single-object-per-step segmentation methods without impairing the scalability, we propose a novel iterative deep reinforcement learning agent that learns how to differentiate multiple objects in parallel. Our reward function for the trainable agent is designed to favor grouping pixels belonging to the same object using a graph coloring algorithm. We demonstrate that the proposed method can efficiently perform instance segmentation of many objects without heavy post-processing.

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arXiv2018

Compressed Sensing MRI Reconstruction using a Generative Adversarial Network with a Cyclic Loss

Compressed Sensing MRI (CS-MRI) has provided theoretical foundations upon which the time-consuming MRI acquisition process can be accelerated. However, it primarily relies on iterative numerical solvers which still hinders their adaptation in time-critical applications. In addition, recent advances in deep neural networks have shown their potential in computer vision and image processing, but their adaptation to MRI reconstruction is still in an early stage. In this paper, we propose a novel deep learning-based generative adversarial model, RefineGAN, for fast and accurate CS-MRI reconstruction. The proposed model is a variant of fully-residual convolutional autoencoder and generative adversarial networks (GANs), specifically designed for CS-MRI formulation; it employs deeper generator and discriminator networks with cyclic data consistency loss for faithful interpolation in the given under-sampled k-space data. In addition, our solution leverages a chained network to further enhance the reconstruction quality. RefineGAN is fast and accurate -- the reconstruction process is extremely rapid, as low as tens of milliseconds for reconstruction of a 256x256 image, because it is one-way deployment on a feed-forward network, and the image quality is superior even for extremely low sampling rate (as low as 10%) due to the data-driven nature of the method. We demonstrate that RefineGAN outperforms the state-of-the-art CS-MRI methods by a large margin in terms of both running time and image quality via evaluation using several open-source MRI databases.

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arXiv2017

ssEMnet: Serial-section Electron Microscopy Image Registration using a Spatial Transformer Network with Learned Features

The alignment of serial-section electron microscopy (ssEM) images is critical for efforts in neuroscience that seek to reconstruct neuronal circuits. However, each ssEM plane contains densely packed structures that vary from one section to the next, which makes matching features across images a challenge. Advances in deep learning has resulted in unprecedented performance in similar computer vision problems, but to our knowledge, they have not been successfully applied to ssEM image co-registration. In this paper, we introduce a novel deep network model that combines a spatial transformer for image deformation and a convolutional autoencoder for unsupervised feature learning for robust ssEM image alignment. This results in improved accuracy and robustness while requiring substantially less user intervention than conventional methods. We evaluate our method by comparing registration quality across several datasets.

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arXiv2016

FusionNet: A deep fully residual convolutional neural network for image segmentation in connectomics

Electron microscopic connectomics is an ambitious research direction with the goal of studying comprehensive brain connectivity maps by using high-throughput, nano-scale microscopy. One of the main challenges in connectomics research is developing scalable image analysis algorithms that require minimal user intervention. Recently, deep learning has drawn much attention in computer vision because of its exceptional performance in image classification tasks. For this reason, its application to connectomic analyses holds great promise, as well. In this paper, we introduce a novel deep neural network architecture, FusionNet, for the automatic segmentation of neuronal structures in connectomics data. FusionNet leverages the latest advances in machine learning, such as semantic segmentation and residual neural networks, with the novel introduction of summation-based skip connections to allow a much deeper network architecture for a more accurate segmentation. We demonstrate the performance of the proposed method by comparing it with state-of-the-art electron microscopy (EM) segmentation methods from the ISBI EM segmentation challenge. We also show the segmentation results on two different tasks including cell membrane and cell body segmentation and a statistical analysis of cell morphology.

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