Won-Dong Jang

Jinyoung Jun, Won-Dong Jang, Wenbin Ouyang et al.

We present FlowFixer, a refinement framework for subject-driven generation (SDG) that restores fine details lost during generation caused by changes in scale and perspective of a subject. FlowFixer proposes direct image-to-image translation from visual references, avoiding ambiguities in language prompts. To enable image-to-image training, we introduce a one-step denoising scheme to generate self-supervised training data, which automatically removes high-frequency details while preserving global structure, effectively simulating real-world SDG errors. We further propose a keypoint matching-based metric to properly assess fidelity in details beyond semantic similarities usually measured by CLIP or DINO. Experimental results demonstrate that FlowFixer outperforms state-of-the-art SDG methods in both qualitative and quantitative evaluations, setting a new benchmark for high-fidelity subject-driven generation.

Anirudh S Chakravarthy, Won-Dong Jang, Zudi Lin et al.

Video instance segmentation aims to detect, segment, and track objects in a video. Current approaches extend image-level segmentation algorithms to the temporal domain. However, this results in temporally inconsistent masks. In this work, we identify the mask quality due to temporal stability as a performance bottleneck. Motivated by this, we propose a video instance segmentation method that alleviates the problem due to missing detections. Since this cannot be solved simply using spatial information, we leverage temporal context using inter-frame attentions. This allows our network to refocus on missing objects using box predictions from the neighbouring frame, thereby overcoming missing detections. Our method significantly outperforms previous state-of-the-art algorithms using the Mask R-CNN backbone, by achieving 36.0% mAP on the YouTube-VIS benchmark. Additionally, our method is completely online and requires no future frames. Our code is publicly available at https://github.com/anirudh-chakravarthy/ObjProp.

Abhimanyu Talwar, Zudi Lin, Donglai Wei et al.

One of the essential tasks in connectomics is the morphology analysis of neurons and organelles like mitochondria to shed light on their biological properties. However, these biological objects often have tangled parts or complex branching patterns, which make it hard to abstract, categorize, and manipulate their morphology. In this paper, we develop a novel topological nomenclature system to name these objects like the appellation for chemical compounds to promote neuroscience analysis based on their skeletal structures. We first convert the volumetric representation into the topology-preserving reduced graph to untangle the objects. Next, we develop nomenclature rules for pyramidal neurons and mitochondria from the reduced graph and finally learn the feature embedding for shape manipulation. In ablation studies, we quantitatively show that graphs generated by our proposed method align with the perception of experts. On 3D shape retrieval and decomposition tasks, we qualitatively demonstrate that the encoded topological nomenclature features achieve better results than state-of-the-art shape descriptors. To advance neuroscience, we will release a 3D segmentation dataset of mitochondria and pyramidal neurons reconstructed from a 100um cube electron microscopy volume with their reduced graph and topological nomenclature annotations. Code is publicly available at https://github.com/donglaiw/ibexHelper.

Stanislav Lukyanenko, Won-Dong Jang, Donglai Wei et al.

The developmental process of embryos follows a monotonic order. An embryo can progressively cleave from one cell to multiple cells and finally transform to morula and blastocyst. For time-lapse videos of embryos, most existing developmental stage classification methods conduct per-frame predictions using an image frame at each time step. However, classification using only images suffers from overlapping between cells and imbalance between stages. Temporal information can be valuable in addressing this problem by capturing movements between neighboring frames. In this work, we propose a two-stream model for developmental stage classification. Unlike previous methods, our two-stream model accepts both temporal and image information. We develop a linear-chain conditional random field (CRF) on top of neural network features extracted from the temporal and image streams to make use of both modalities. The linear-chain CRF formulation enables tractable training of global sequential models over multiple frames while also making it possible to inject monotonic development order constraints into the learning process explicitly. We demonstrate our algorithm on two time-lapse embryo video datasets: i) mouse and ii) human embryo datasets. Our method achieves 98.1 % and 80.6 % for mouse and human embryo stage classification, respectively. Our approach will enable more profound clinical and biological studies and suggests a new direction for developmental stage classification by utilizing temporal information.

Won-Dong Jang, Donglai Wei, Xingxuan Zhang et al.

Blastomere instance segmentation is important for analyzing embryos' abnormality. To measure the accurate shapes and sizes of blastomeres, their amodal segmentation is necessary. Amodal instance segmentation aims to recover the complete silhouette of an object even when the object is not fully visible. For each detected object, previous methods directly regress the target mask from input features. However, images of an object under different amounts of occlusion should have the same amodal mask output, which makes it harder to train the regression model. To alleviate the problem, we propose to classify input features into intermediate shape codes and recover complete object shapes from them. First, we pre-train the Vector Quantized Variational Autoencoder (VQ-VAE) model to learn these discrete shape codes from ground truth amodal masks. Then, we incorporate the VQ-VAE model into the amodal instance segmentation pipeline with an additional refinement module. We also detect an occlusion map to integrate occlusion information with a backbone feature. As such, our network faithfully detects bounding boxes of amodal objects. On an internal embryo cell image benchmark, the proposed method outperforms previous state-of-the-art methods. To show generalizability, we show segmentation results on the public KINS natural image benchmark. To examine the learned shape codes and model design choices, we perform ablation studies on a synthetic dataset of simple overlaid shapes. Our method would enable accurate measurement of blastomeres in in vitro fertilization (IVF) clinics, which potentially can increase IVF success rate.

Brian D. Leahy, Won-Dong Jang, Helen Y. Yang et al.

A major challenge in clinical In-Vitro Fertilization (IVF) is selecting the highest quality embryo to transfer to the patient in the hopes of achieving a pregnancy. Time-lapse microscopy provides clinicians with a wealth of information for selecting embryos. However, the resulting movies of embryos are currently analyzed manually, which is time consuming and subjective. Here, we automate feature extraction of time-lapse microscopy of human embryos with a machine-learning pipeline of five convolutional neural networks (CNNs). Our pipeline consists of (1) semantic segmentation of the regions of the embryo, (2) regression predictions of fragment severity, (3) classification of the developmental stage, and object instance segmentation of (4) cells and (5) pronuclei. Our approach greatly speeds up the measurement of quantitative, biologically relevant features that may aid in embryo selection.