arXiv subjects

Mengwei Ren

Publications and source records attributed to Mengwei Ren.

26 records · Page 2Linked to original sources

arXiv2023

Microscopy Image Segmentation via Point and Shape Regularized Data Synthesis

Current deep learning-based approaches for the segmentation of microscopy images heavily rely on large amount of training data with dense annotation, which is highly costly and laborious in practice. Compared to full annotation where the complete contour of objects is depicted, point annotations, specifically object centroids, are much easier to acquire and still provide crucial information about the objects for subsequent segmentation. In this paper, we assume access to point annotations only during training and develop a unified pipeline for microscopy image segmentation using synthetically generated training data. Our framework includes three stages: (1) it takes point annotations and samples a pseudo dense segmentation mask constrained with shape priors; (2) with an image generative model trained in an unpaired manner, it translates the mask to a realistic microscopy image regularized by object level consistency; (3) the pseudo masks along with the synthetic images then constitute a pairwise dataset for training an ad-hoc segmentation model. On the public MoNuSeg dataset, our synthesis pipeline produces more diverse and realistic images than baseline models while maintaining high coherence between input masks and generated images. When using the identical segmentation backbones, the models trained on our synthetic dataset significantly outperform those trained with pseudo-labels or baseline-generated images. Moreover, our framework achieves comparable results to models trained on authentic microscopy images with dense labels, demonstrating its potential as a reliable and highly efficient alternative to labor-intensive manual pixel-wise annotations in microscopy image segmentation. The code is available.

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arXiv2023

Keypoint-Augmented Self-Supervised Learning for Medical Image Segmentation with Limited Annotation

Pretraining CNN models (i.e., UNet) through self-supervision has become a powerful approach to facilitate medical image segmentation under low annotation regimes. Recent contrastive learning methods encourage similar global representations when the same image undergoes different transformations, or enforce invariance across different image/patch features that are intrinsically correlated. However, CNN-extracted global and local features are limited in capturing long-range spatial dependencies that are essential in biological anatomy. To this end, we present a keypoint-augmented fusion layer that extracts representations preserving both short- and long-range self-attention. In particular, we augment the CNN feature map at multiple scales by incorporating an additional input that learns long-range spatial self-attention among localized keypoint features. Further, we introduce both global and local self-supervised pretraining for the framework. At the global scale, we obtain global representations from both the bottleneck of the UNet, and by aggregating multiscale keypoint features. These global features are subsequently regularized through image-level contrastive objectives. At the local scale, we define a distance-based criterion to first establish correspondences among keypoints and encourage similarity between their features. Through extensive experiments on both MRI and CT segmentation tasks, we demonstrate the architectural advantages of our proposed method in comparison to both CNN and Transformer-based UNets, when all architectures are trained with randomly initialized weights. With our proposed pretraining strategy, our method further outperforms existing SSL methods by producing more robust self-attention and achieving state-of-the-art segmentation results. The code is available at https://github.com/zshyang/kaf.git.

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arXiv2023

Improving Tuning-Free Real Image Editing with Proximal Guidance

DDIM inversion has revealed the remarkable potential of real image editing within diffusion-based methods. However, the accuracy of DDIM reconstruction degrades as larger classifier-free guidance (CFG) scales being used for enhanced editing. Null-text inversion (NTI) optimizes null embeddings to align the reconstruction and inversion trajectories with larger CFG scales, enabling real image editing with cross-attention control. Negative-prompt inversion (NPI) further offers a training-free closed-form solution of NTI. However, it may introduce artifacts and is still constrained by DDIM reconstruction quality. To overcome these limitations, we propose proximal guidance and incorporate it to NPI with cross-attention control. We enhance NPI with a regularization term and reconstruction guidance, which reduces artifacts while capitalizing on its training-free nature. Additionally, we extend the concepts to incorporate mutual self-attention control, enabling geometry and layout alterations in the editing process. Our method provides an efficient and straightforward approach, effectively addressing real image editing tasks with minimal computational overhead.

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arXiv2022

Generative Adversarial Registration for Improved Conditional Deformable Templates

Deformable templates are essential to large-scale medical image registration, segmentation, and population analysis. Current conventional and deep network-based methods for template construction use only regularized registration objectives and often yield templates with blurry and/or anatomically implausible appearance, confounding downstream biomedical interpretation. We reformulate deformable registration and conditional template estimation as an adversarial game wherein we encourage realism in the moved templates with a generative adversarial registration framework conditioned on flexible image covariates. The resulting templates exhibit significant gain in specificity to attributes such as age and disease, better fit underlying group-wise spatiotemporal trends, and achieve improved sharpness and centrality. These improvements enable more accurate population modeling with diverse covariates for standardized downstream analyses and easier anatomical delineation for structures of interest.

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arXiv2021

Q-space Conditioned Translation Networks for Directional Synthesis of Diffusion Weighted Images from Multi-modal Structural MRI

Current deep learning approaches for diffusion MRI modeling circumvent the need for densely-sampled diffusion-weighted images (DWIs) by directly predicting microstructural indices from sparsely-sampled DWIs. However, they implicitly make unrealistic assumptions of static $q$-space sampling during training and reconstruction. Further, such approaches can restrict downstream usage of variably sampled DWIs for usages including the estimation of microstructural indices or tractography. We propose a generative adversarial translation framework for high-quality DWI synthesis with arbitrary $q$-space sampling given commonly acquired structural images (e.g., B0, T1, T2). Our translation network linearly modulates its internal representations conditioned on continuous $q$-space information, thus removing the need for fixed sampling schemes. Moreover, this approach enables downstream estimation of high-quality microstructural maps from arbitrarily subsampled DWIs, which may be particularly important in cases with sparsely sampled DWIs. Across several recent methodologies, the proposed approach yields improved DWI synthesis accuracy and fidelity with enhanced downstream utility as quantified by the accuracy of scalar microstructure indices estimated from the synthesized images. Code is available at https://github.com/mengweiren/q-space-conditioned-dwi-synthesis.

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arXiv2021

Segmentation-Renormalized Deep Feature Modulation for Unpaired Image Harmonization

Deep networks are now ubiquitous in large-scale multi-center imaging studies. However, the direct aggregation of images across sites is contraindicated for downstream statistical and deep learning-based image analysis due to inconsistent contrast, resolution, and noise. To this end, in the absence of paired data, variations of Cycle-consistent Generative Adversarial Networks have been used to harmonize image sets between a source and target domain. Importantly, these methods are prone to instability, contrast inversion, intractable manipulation of pathology, and steganographic mappings which limit their reliable adoption in real-world medical imaging. In this work, based on an underlying assumption that morphological shape is consistent across imaging sites, we propose a segmentation-renormalized image translation framework to reduce inter-scanner heterogeneity while preserving anatomical layout. We replace the affine transformations used in the normalization layers within generative networks with trainable scale and shift parameters conditioned on jointly learned anatomical segmentation embeddings to modulate features at every level of translation. We evaluate our methodologies against recent baselines across several imaging modalities (T1w MRI, FLAIR MRI, and OCT) on datasets with and without lesions. Segmentation-renormalization for translation GANs yields superior image harmonization as quantified by Inception distances, demonstrates improved downstream utility via post-hoc segmentation accuracy, and improved robustness to translation perturbation and self-adversarial attacks.

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arXiv2019

Structure-Attentioned Memory Network for Monocular Depth Estimation

Monocular depth estimation is a challenging task that aims to predict a corresponding depth map from a given single RGB image. Recent deep learning models have been proposed to predict the depth from the image by learning the alignment of deep features between the RGB image and the depth domains. In this paper, we present a novel approach, named Structure-Attentioned Memory Network, to more effectively transfer domain features for monocular depth estimation by taking into account the common structure regularities (e.g., repetitive structure patterns, planar surfaces, symmetries) in domain adaptation. To this end, we introduce a new Structure-Oriented Memory (SOM) module to learn and memorize the structure-specific information between RGB image domain and the depth domain. More specifically, in the SOM module, we develop a Memorable Bank of Filters (MBF) unit to learn a set of filters that memorize the structure-aware image-depth residual pattern, and also an Attention Guided Controller (AGC) unit to control the filter selection in the MBF given image features queries. Given the query image feature, the trained SOM module is able to adaptively select the best customized filters for cross-domain feature transferring with an optimal structural disparity between image and depth. In summary, we focus on addressing this structure-specific domain adaption challenge by proposing a novel end-to-end multi-scale memorable network for monocular depth estimation. The experiments show that our proposed model demonstrates the superior performance compared to the existing supervised monocular depth estimation approaches on the challenging KITTI and NYU Depth V2 benchmarks.

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arXiv2017

3D-A-Nets: 3D Deep Dense Descriptor for Volumetric Shapes with Adversarial Networks

Recently researchers have been shifting their focus towards learned 3D shape descriptors from hand-craft ones to better address challenging issues of the deformation and structural variation inherently present in 3D objects. 3D geometric data are often transformed to 3D Voxel grids with regular format in order to be better fed to a deep neural net architecture. However, the computational intractability of direct application of 3D convolutional nets to 3D volumetric data severely limits the efficiency (i.e. slow processing) and effectiveness (i.e. unsatisfied accuracy) in processing 3D geometric data. In this paper, powered with a novel design of adversarial networks (3D-A-Nets), we have developed a novel 3D deep dense shape descriptor (3D-DDSD) to address the challenging issues of efficient and effective 3D volumetric data processing. We developed new definition of 2D multilayer dense representation (MDR) of 3D volumetric data to extract concise but geometrically informative shape description and a novel design of adversarial networks that jointly train a set of convolution neural network (CNN), recurrent neural network (RNN) and an adversarial discriminator. More specifically, the generator network produces 3D shape features that encourages the clustering of samples from the same category with correct class label, whereas the discriminator network discourages the clustering by assigning them misleading adversarial class labels. By addressing the challenges posed by the computational inefficiency of direct application of CNN to 3D volumetric data, 3D-A-Nets can learn high-quality 3D-DSDD which demonstrates superior performance on 3D shape classification and retrieval over other state-of-the-art techniques by a great margin.

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