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Dec 31

MeshMamba: State Space Models for Articulated 3D Mesh Generation and Reconstruction

In this paper, we introduce MeshMamba, a neural network model for learning 3D articulated mesh models by employing the recently proposed Mamba State Space Models (Mamba-SSMs). MeshMamba is efficient and scalable in handling a large number of input tokens, enabling the generation and reconstruction of body mesh models with more than 10,000 vertices, capturing clothing and hand geometries. The key to effectively learning MeshMamba is the serialization technique of mesh vertices into orderings that are easily processed by Mamba. This is achieved by sorting the vertices based on body part annotations or the 3D vertex locations of a template mesh, such that the ordering respects the structure of articulated shapes. Based on MeshMamba, we design 1) MambaDiff3D, a denoising diffusion model for generating 3D articulated meshes and 2) Mamba-HMR, a 3D human mesh recovery model that reconstructs a human body shape and pose from a single image. Experimental results showed that MambaDiff3D can generate dense 3D human meshes in clothes, with grasping hands, etc., and outperforms previous approaches in the 3D human shape generation task. Additionally, Mamba-HMR extends the capabilities of previous non-parametric human mesh recovery approaches, which were limited to handling body-only poses using around 500 vertex tokens, to the whole-body setting with face and hands, while achieving competitive performance in (near) real-time.

  • 3 authors
·
Jul 20

AGHI-QA: A Subjective-Aligned Dataset and Metric for AI-Generated Human Images

The rapid development of text-to-image (T2I) generation approaches has attracted extensive interest in evaluating the quality of generated images, leading to the development of various quality assessment methods for general-purpose T2I outputs. However, existing image quality assessment (IQA) methods are limited to providing global quality scores, failing to deliver fine-grained perceptual evaluations for structurally complex subjects like humans, which is a critical challenge considering the frequent anatomical and textural distortions in AI-generated human images (AGHIs). To address this gap, we introduce AGHI-QA, the first large-scale benchmark specifically designed for quality assessment of AGHIs. The dataset comprises 4,000 images generated from 400 carefully crafted text prompts using 10 state of-the-art T2I models. We conduct a systematic subjective study to collect multidimensional annotations, including perceptual quality scores, text-image correspondence scores, visible and distorted body part labels. Based on AGHI-QA, we evaluate the strengths and weaknesses of current T2I methods in generating human images from multiple dimensions. Furthermore, we propose AGHI-Assessor, a novel quality metric that integrates the large multimodal model (LMM) with domain-specific human features for precise quality prediction and identification of visible and distorted body parts in AGHIs. Extensive experimental results demonstrate that AGHI-Assessor showcases state-of-the-art performance, significantly outperforming existing IQA methods in multidimensional quality assessment and surpassing leading LMMs in detecting structural distortions in AGHIs.

  • 9 authors
·
Apr 30

DOPE: Distillation Of Part Experts for whole-body 3D pose estimation in the wild

We introduce DOPE, the first method to detect and estimate whole-body 3D human poses, including bodies, hands and faces, in the wild. Achieving this level of details is key for a number of applications that require understanding the interactions of the people with each other or with the environment. The main challenge is the lack of in-the-wild data with labeled whole-body 3D poses. In previous work, training data has been annotated or generated for simpler tasks focusing on bodies, hands or faces separately. In this work, we propose to take advantage of these datasets to train independent experts for each part, namely a body, a hand and a face expert, and distill their knowledge into a single deep network designed for whole-body 2D-3D pose detection. In practice, given a training image with partial or no annotation, each part expert detects its subset of keypoints in 2D and 3D and the resulting estimations are combined to obtain whole-body pseudo ground-truth poses. A distillation loss encourages the whole-body predictions to mimic the experts' outputs. Our results show that this approach significantly outperforms the same whole-body model trained without distillation while staying close to the performance of the experts. Importantly, DOPE is computationally less demanding than the ensemble of experts and can achieve real-time performance. Test code and models are available at https://europe.naverlabs.com/research/computer-vision/dope.

  • 5 authors
·
Aug 21, 2020

Detecting Human-Object Contact in Images

Humans constantly contact objects to move and perform tasks. Thus, detecting human-object contact is important for building human-centered artificial intelligence. However, there exists no robust method to detect contact between the body and the scene from an image, and there exists no dataset to learn such a detector. We fill this gap with HOT ("Human-Object conTact"), a new dataset of human-object contacts for images. To build HOT, we use two data sources: (1) We use the PROX dataset of 3D human meshes moving in 3D scenes, and automatically annotate 2D image areas for contact via 3D mesh proximity and projection. (2) We use the V-COCO, HAKE and Watch-n-Patch datasets, and ask trained annotators to draw polygons for the 2D image areas where contact takes place. We also annotate the involved body part of the human body. We use our HOT dataset to train a new contact detector, which takes a single color image as input, and outputs 2D contact heatmaps as well as the body-part labels that are in contact. This is a new and challenging task that extends current foot-ground or hand-object contact detectors to the full generality of the whole body. The detector uses a part-attention branch to guide contact estimation through the context of the surrounding body parts and scene. We evaluate our detector extensively, and quantitative results show that our model outperforms baselines, and that all components contribute to better performance. Results on images from an online repository show reasonable detections and generalizability.

  • 4 authors
·
Mar 6, 2023

Detailed Annotations of Chest X-Rays via CT Projection for Report Understanding

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

  • 10 authors
·
Oct 7, 2022

One-Stage 3D Whole-Body Mesh Recovery with Component Aware Transformer

Whole-body mesh recovery aims to estimate the 3D human body, face, and hands parameters from a single image. It is challenging to perform this task with a single network due to resolution issues, i.e., the face and hands are usually located in extremely small regions. Existing works usually detect hands and faces, enlarge their resolution to feed in a specific network to predict the parameter, and finally fuse the results. While this copy-paste pipeline can capture the fine-grained details of the face and hands, the connections between different parts cannot be easily recovered in late fusion, leading to implausible 3D rotation and unnatural pose. In this work, we propose a one-stage pipeline for expressive whole-body mesh recovery, named OSX, without separate networks for each part. Specifically, we design a Component Aware Transformer (CAT) composed of a global body encoder and a local face/hand decoder. The encoder predicts the body parameters and provides a high-quality feature map for the decoder, which performs a feature-level upsample-crop scheme to extract high-resolution part-specific features and adopt keypoint-guided deformable attention to estimate hand and face precisely. The whole pipeline is simple yet effective without any manual post-processing and naturally avoids implausible prediction. Comprehensive experiments demonstrate the effectiveness of OSX. Lastly, we build a large-scale Upper-Body dataset (UBody) with high-quality 2D and 3D whole-body annotations. It contains persons with partially visible bodies in diverse real-life scenarios to bridge the gap between the basic task and downstream applications.

  • 5 authors
·
Mar 28, 2023

Holistic Understanding of 3D Scenes as Universal Scene Description

3D scene understanding is a long-standing challenge in computer vision and a key component in enabling mixed reality, wearable computing, and embodied AI. Providing a solution to these applications requires a multifaceted approach that covers scene-centric, object-centric, as well as interaction-centric capabilities. While there exist numerous datasets approaching the former two problems, the task of understanding interactable and articulated objects is underrepresented and only partly covered by current works. In this work, we address this shortcoming and introduce (1) an expertly curated dataset in the Universal Scene Description (USD) format, featuring high-quality manual annotations, for instance, segmentation and articulation on 280 indoor scenes; (2) a learning-based model together with a novel baseline capable of predicting part segmentation along with a full specification of motion attributes, including motion type, articulated and interactable parts, and motion parameters; (3) a benchmark serving to compare upcoming methods for the task at hand. Overall, our dataset provides 8 types of annotations - object and part segmentations, motion types, movable and interactable parts, motion parameters, connectivity, and object mass annotations. With its broad and high-quality annotations, the data provides the basis for holistic 3D scene understanding models. All data is provided in the USD format, allowing interoperability and easy integration with downstream tasks. We provide open access to our dataset, benchmark, and method's source code.

  • 6 authors
·
Dec 2, 2024

BPJDet: Extended Object Representation for Generic Body-Part Joint Detection

Detection of human body and its parts (e.g., head or hands) has been intensively studied. However, most of these CNNs-based detectors are trained independently, making it difficult to associate detected parts with body. In this paper, we focus on the joint detection of human body and its corresponding parts. Specifically, we propose a novel extended object representation integrating center-offsets of body parts, and construct a dense one-stage generic Body-Part Joint Detector (BPJDet). In this way, body-part associations are neatly embedded in a unified object representation containing both semantic and geometric contents. Therefore, we can perform multi-loss optimizations to tackle multi-tasks synergistically. BPJDet does not suffer from error-prone post matching, and keeps a better trade-off between speed and accuracy. Furthermore, BPJDet can be generalized to detect any one or more body parts. To verify the superiority of BPJDet, we conduct experiments on three body-part datasets (CityPersons, CrowdHuman and BodyHands) and one body-parts dataset COCOHumanParts. While keeping high detection accuracy, BPJDet achieves state-of-the-art association performance on all datasets comparing with its counterparts. Besides, we show benefits of advanced body-part association capability by improving performance of two representative downstream applications: accurate crowd head detection and hand contact estimation. Code is released in https://github.com/hnuzhy/BPJDet.

  • 5 authors
·
Apr 21, 2023

Effective Whole-body Pose Estimation with Two-stages Distillation

Whole-body pose estimation localizes the human body, hand, face, and foot keypoints in an image. This task is challenging due to multi-scale body parts, fine-grained localization for low-resolution regions, and data scarcity. Meanwhile, applying a highly efficient and accurate pose estimator to widely human-centric understanding and generation tasks is urgent. In this work, we present a two-stage pose Distillation for Whole-body Pose estimators, named DWPose, to improve their effectiveness and efficiency. The first-stage distillation designs a weight-decay strategy while utilizing a teacher's intermediate feature and final logits with both visible and invisible keypoints to supervise the student from scratch. The second stage distills the student model itself to further improve performance. Different from the previous self-knowledge distillation, this stage finetunes the student's head with only 20% training time as a plug-and-play training strategy. For data limitations, we explore the UBody dataset that contains diverse facial expressions and hand gestures for real-life applications. Comprehensive experiments show the superiority of our proposed simple yet effective methods. We achieve new state-of-the-art performance on COCO-WholeBody, significantly boosting the whole-body AP of RTMPose-l from 64.8% to 66.5%, even surpassing RTMPose-x teacher with 65.3% AP. We release a series of models with different sizes, from tiny to large, for satisfying various downstream tasks. Our codes and models are available at https://github.com/IDEA-Research/DWPose.

  • 4 authors
·
Jul 28, 2023

RTMW: Real-Time Multi-Person 2D and 3D Whole-body Pose Estimation

Whole-body pose estimation is a challenging task that requires simultaneous prediction of keypoints for the body, hands, face, and feet. Whole-body pose estimation aims to predict fine-grained pose information for the human body, including the face, torso, hands, and feet, which plays an important role in the study of human-centric perception and generation and in various applications. In this work, we present RTMW (Real-Time Multi-person Whole-body pose estimation models), a series of high-performance models for 2D/3D whole-body pose estimation. We incorporate RTMPose model architecture with FPN and HEM (Hierarchical Encoding Module) to better capture pose information from different body parts with various scales. The model is trained with a rich collection of open-source human keypoint datasets with manually aligned annotations and further enhanced via a two-stage distillation strategy. RTMW demonstrates strong performance on multiple whole-body pose estimation benchmarks while maintaining high inference efficiency and deployment friendliness. We release three sizes: m/l/x, with RTMW-l achieving a 70.2 mAP on the COCO-Wholebody benchmark, making it the first open-source model to exceed 70 mAP on this benchmark. Meanwhile, we explored the performance of RTMW in the task of 3D whole-body pose estimation, conducting image-based monocular 3D whole-body pose estimation in a coordinate classification manner. We hope this work can benefit both academic research and industrial applications. The code and models have been made publicly available at: https://github.com/open-mmlab/mmpose/tree/main/projects/rtmpose

  • 3 authors
·
Jul 11, 2024 1

Look into Person: Joint Body Parsing & Pose Estimation Network and A New Benchmark

Human parsing and pose estimation have recently received considerable interest due to their substantial application potentials. However, the existing datasets have limited numbers of images and annotations and lack a variety of human appearances and coverage of challenging cases in unconstrained environments. In this paper, we introduce a new benchmark named "Look into Person (LIP)" that provides a significant advancement in terms of scalability, diversity, and difficulty, which are crucial for future developments in human-centric analysis. This comprehensive dataset contains over 50,000 elaborately annotated images with 19 semantic part labels and 16 body joints, which are captured from a broad range of viewpoints, occlusions, and background complexities. Using these rich annotations, we perform detailed analyses of the leading human parsing and pose estimation approaches, thereby obtaining insights into the successes and failures of these methods. To further explore and take advantage of the semantic correlation of these two tasks, we propose a novel joint human parsing and pose estimation network to explore efficient context modeling, which can simultaneously predict parsing and pose with extremely high quality. Furthermore, we simplify the network to solve human parsing by exploring a novel self-supervised structure-sensitive learning approach, which imposes human pose structures into the parsing results without resorting to extra supervision. The dataset, code and models are available at http://www.sysu-hcp.net/lip/.

  • 4 authors
·
Apr 5, 2018

TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

  • 12 authors
·
Aug 11, 2022

HOT3D: Hand and Object Tracking in 3D from Egocentric Multi-View Videos

We introduce HOT3D, a publicly available dataset for egocentric hand and object tracking in 3D. The dataset offers over 833 minutes (more than 3.7M images) of multi-view RGB/monochrome image streams showing 19 subjects interacting with 33 diverse rigid objects, multi-modal signals such as eye gaze or scene point clouds, as well as comprehensive ground-truth annotations including 3D poses of objects, hands, and cameras, and 3D models of hands and objects. In addition to simple pick-up/observe/put-down actions, HOT3D contains scenarios resembling typical actions in a kitchen, office, and living room environment. The dataset is recorded by two head-mounted devices from Meta: Project Aria, a research prototype of light-weight AR/AI glasses, and Quest 3, a production VR headset sold in millions of units. Ground-truth poses were obtained by a professional motion-capture system using small optical markers attached to hands and objects. Hand annotations are provided in the UmeTrack and MANO formats and objects are represented by 3D meshes with PBR materials obtained by an in-house scanner. In our experiments, we demonstrate the effectiveness of multi-view egocentric data for three popular tasks: 3D hand tracking, 6DoF object pose estimation, and 3D lifting of unknown in-hand objects. The evaluated multi-view methods, whose benchmarking is uniquely enabled by HOT3D, significantly outperform their single-view counterparts.

  • 14 authors
·
Nov 28, 2024

PoseScript: Linking 3D Human Poses and Natural Language

Natural language plays a critical role in many computer vision applications, such as image captioning, visual question answering, and cross-modal retrieval, to provide fine-grained semantic information. Unfortunately, while human pose is key to human understanding, current 3D human pose datasets lack detailed language descriptions. To address this issue, we have introduced the PoseScript dataset. This dataset pairs more than six thousand 3D human poses from AMASS with rich human-annotated descriptions of the body parts and their spatial relationships. Additionally, to increase the size of the dataset to a scale that is compatible with data-hungry learning algorithms, we have proposed an elaborate captioning process that generates automatic synthetic descriptions in natural language from given 3D keypoints. This process extracts low-level pose information, known as "posecodes", using a set of simple but generic rules on the 3D keypoints. These posecodes are then combined into higher level textual descriptions using syntactic rules. With automatic annotations, the amount of available data significantly scales up (100k), making it possible to effectively pretrain deep models for finetuning on human captions. To showcase the potential of annotated poses, we present three multi-modal learning tasks that utilize the PoseScript dataset. Firstly, we develop a pipeline that maps 3D poses and textual descriptions into a joint embedding space, allowing for cross-modal retrieval of relevant poses from large-scale datasets. Secondly, we establish a baseline for a text-conditioned model generating 3D poses. Thirdly, we present a learned process for generating pose descriptions. These applications demonstrate the versatility and usefulness of annotated poses in various tasks and pave the way for future research in the field.

  • 5 authors
·
Oct 21, 2022

hSDB-instrument: Instrument Localization Database for Laparoscopic and Robotic Surgeries

Automated surgical instrument localization is an important technology to understand the surgical process and in order to analyze them to provide meaningful guidance during surgery or surgical index after surgery to the surgeon. We introduce a new dataset that reflects the kinematic characteristics of surgical instruments for automated surgical instrument localization of surgical videos. The hSDB(hutom Surgery DataBase)-instrument dataset consists of instrument localization information from 24 cases of laparoscopic cholecystecomy and 24 cases of robotic gastrectomy. Localization information for all instruments is provided in the form of a bounding box for object detection. To handle class imbalance problem between instruments, synthesized instruments modeled in Unity for 3D models are included as training data. Besides, for 3D instrument data, a polygon annotation is provided to enable instance segmentation of the tool. To reflect the kinematic characteristics of all instruments, they are annotated with head and body parts for laparoscopic instruments, and with head, wrist, and body parts for robotic instruments separately. Annotation data of assistive tools (specimen bag, needle, etc.) that are frequently used for surgery are also included. Moreover, we provide statistical information on the hSDB-instrument dataset and the baseline localization performances of the object detection networks trained by the MMDetection library and resulting analyses.

  • 12 authors
·
Oct 24, 2021

NCL-SM: A Fully Annotated Dataset of Images from Human Skeletal Muscle Biopsies

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

  • 7 authors
·
Nov 25, 2023

AiOS: All-in-One-Stage Expressive Human Pose and Shape Estimation

Expressive human pose and shape estimation (a.k.a. 3D whole-body mesh recovery) involves the human body, hand, and expression estimation. Most existing methods have tackled this task in a two-stage manner, first detecting the human body part with an off-the-shelf detection model and inferring the different human body parts individually. Despite the impressive results achieved, these methods suffer from 1) loss of valuable contextual information via cropping, 2) introducing distractions, and 3) lacking inter-association among different persons and body parts, inevitably causing performance degradation, especially for crowded scenes. To address these issues, we introduce a novel all-in-one-stage framework, AiOS, for multiple expressive human pose and shape recovery without an additional human detection step. Specifically, our method is built upon DETR, which treats multi-person whole-body mesh recovery task as a progressive set prediction problem with various sequential detection. We devise the decoder tokens and extend them to our task. Specifically, we first employ a human token to probe a human location in the image and encode global features for each instance, which provides a coarse location for the later transformer block. Then, we introduce a joint-related token to probe the human joint in the image and encoder a fine-grained local feature, which collaborates with the global feature to regress the whole-body mesh. This straightforward but effective model outperforms previous state-of-the-art methods by a 9% reduction in NMVE on AGORA, a 30% reduction in PVE on EHF, a 10% reduction in PVE on ARCTIC, and a 3% reduction in PVE on EgoBody.

  • 11 authors
·
Mar 26, 2024 1

SINC: Spatial Composition of 3D Human Motions for Simultaneous Action Generation

Our goal is to synthesize 3D human motions given textual inputs describing simultaneous actions, for example 'waving hand' while 'walking' at the same time. We refer to generating such simultaneous movements as performing 'spatial compositions'. In contrast to temporal compositions that seek to transition from one action to another, spatial compositing requires understanding which body parts are involved in which action, to be able to move them simultaneously. Motivated by the observation that the correspondence between actions and body parts is encoded in powerful language models, we extract this knowledge by prompting GPT-3 with text such as "what are the body parts involved in the action <action name>?", while also providing the parts list and few-shot examples. Given this action-part mapping, we combine body parts from two motions together and establish the first automated method to spatially compose two actions. However, training data with compositional actions is always limited by the combinatorics. Hence, we further create synthetic data with this approach, and use it to train a new state-of-the-art text-to-motion generation model, called SINC ("SImultaneous actioN Compositions for 3D human motions"). In our experiments, that training with such GPT-guided synthetic data improves spatial composition generation over baselines. Our code is publicly available at https://sinc.is.tue.mpg.de/.

  • 4 authors
·
Apr 20, 2023

Refinement Module based on Parse Graph of Feature Map for Human Pose Estimation

Parse graphs of the human body can be obtained in the human brain to help humans complete the human pose estimation (HPE). It contains a hierarchical structure, like a tree structure, and context relations among nodes. Many researchers pre-design the parse graph of body structure, and then design framework for HPE. However, these frameworks are difficulty adapting when encountering situations that differ from the preset human structure. Different from them, we regard the feature map as a whole, similarly to human body, so the feature map can be optimized based on parse graphs and each node feature is learned implicitly instead of explicitly, which means it can flexibly respond to different human body structure. In this paper, we design the Refinement Module based on the Parse Graph of feature map (RMPG), which includes two stages: top-down decomposition and bottom-up combination. In the top-down decomposition stage, the feature map is decomposed into multiple sub-feature maps along the channel and their context relations are calculated to obtain their respective context information. In the bottom-up combination stage, the sub-feature maps and their context information are combined to obtain refined sub-feature maps, and then these refined sub-feature maps are concatenated to obtain the refined feature map. Additionally ,we design a top-down framework by using multiple RMPG modules for HPE, some of which are supervised to obtain context relations among body parts. Our framework achieves excellent results on the COCO keypoint detection, CrowdPose and MPII human pose datasets. More importantly, our experiments also demonstrate the effectiveness of RMPG on different methods, including SimpleBaselines, Hourglass, and ViTPose.

  • 3 authors
·
Jan 19

Label Critic: Design Data Before Models

As medical datasets rapidly expand, creating detailed annotations of different body structures becomes increasingly expensive and time-consuming. We consider that requesting radiologists to create detailed annotations is unnecessarily burdensome and that pre-existing AI models can largely automate this process. Following the spirit don't use a sledgehammer on a nut, we find that, rather than creating annotations from scratch, radiologists only have to review and edit errors if the Best-AI Labels have mistakes. To obtain the Best-AI Labels among multiple AI Labels, we developed an automatic tool, called Label Critic, that can assess label quality through tireless pairwise comparisons. Extensive experiments demonstrate that, when incorporated with our developed Image-Prompt pairs, pre-existing Large Vision-Language Models (LVLM), trained on natural images and texts, achieve 96.5% accuracy when choosing the best label in a pair-wise comparison, without extra fine-tuning. By transforming the manual annotation task (30-60 min/scan) into an automatic comparison task (15 sec/scan), we effectively reduce the manual efforts required from radiologists by an order of magnitude. When the Best-AI Labels are sufficiently accurate (81% depending on body structures), they will be directly adopted as the gold-standard annotations for the dataset, with lower-quality AI Labels automatically discarded. Label Critic can also check the label quality of a single AI Label with 71.8% accuracy when no alternatives are available for comparison, prompting radiologists to review and edit if the estimated quality is low (19% depending on body structures).

  • 7 authors
·
Nov 4, 2024

ATLAS: Decoupling Skeletal and Shape Parameters for Expressive Parametric Human Modeling

Parametric body models offer expressive 3D representation of humans across a wide range of poses, shapes, and facial expressions, typically derived by learning a basis over registered 3D meshes. However, existing human mesh modeling approaches struggle to capture detailed variations across diverse body poses and shapes, largely due to limited training data diversity and restrictive modeling assumptions. Moreover, the common paradigm first optimizes the external body surface using a linear basis, then regresses internal skeletal joints from surface vertices. This approach introduces problematic dependencies between internal skeleton and outer soft tissue, limiting direct control over body height and bone lengths. To address these issues, we present ATLAS, a high-fidelity body model learned from 600k high-resolution scans captured using 240 synchronized cameras. Unlike previous methods, we explicitly decouple the shape and skeleton bases by grounding our mesh representation in the human skeleton. This decoupling enables enhanced shape expressivity, fine-grained customization of body attributes, and keypoint fitting independent of external soft-tissue characteristics. ATLAS outperforms existing methods by fitting unseen subjects in diverse poses more accurately, and quantitative evaluations show that our non-linear pose correctives more effectively capture complex poses compared to linear models.

MRSegmentator: Robust Multi-Modality Segmentation of 40 Classes in MRI and CT Sequences

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

  • 11 authors
·
May 10, 2024

Name That Part: 3D Part Segmentation and Naming

We address semantic 3D part segmentation: decomposing objects into parts with meaningful names. While datasets exist with part annotations, their definitions are inconsistent across datasets, limiting robust training. Previous methods produce unlabeled decompositions or retrieve single parts without complete shape annotations. We propose ALIGN-Parts, which formulates part naming as a direct set alignment task. Our method decomposes shapes into partlets - implicit 3D part representations - matched to part descriptions via bipartite assignment. We combine geometric cues from 3D part fields, appearance from multi-view vision features, and semantic knowledge from language-model-generated affordance descriptions. Text-alignment loss ensures partlets share embedding space with text, enabling a theoretically open-vocabulary matching setup, given sufficient data. Our efficient and novel, one-shot, 3D part segmentation and naming method finds applications in several downstream tasks, including serving as a scalable annotation engine. As our model supports zero-shot matching to arbitrary descriptions and confidence-calibrated predictions for known categories, with human verification, we create a unified ontology that aligns PartNet, 3DCoMPaT++, and Find3D, consisting of 1,794 unique 3D parts. We also show examples from our newly created Tex-Parts dataset. We also introduce 2 novel metrics appropriate for the named 3D part segmentation task.

  • 5 authors
·
Dec 19 2

Detecting automatically the layout of clinical documents to enhance the performances of downstream natural language processing

Objective:Develop and validate an algorithm for analyzing the layout of PDF clinical documents to improve the performance of downstream natural language processing tasks. Materials and Methods: We designed an algorithm to process clinical PDF documents and extract only clinically relevant text. The algorithm consists of several steps: initial text extraction using a PDF parser, followed by classification into categories such as body text, left notes, and footers using a Transformer deep neural network architecture, and finally an aggregation step to compile the lines of a given label in the text. We evaluated the technical performance of the body text extraction algorithm by applying it to a random sample of documents that were annotated. Medical performance was evaluated by examining the extraction of medical concepts of interest from the text in their respective sections. Finally, we tested an end-to-end system on a medical use case of automatic detection of acute infection described in the hospital report. Results:Our algorithm achieved per-line precision, recall, and F1 score of 98.4, 97.0, and 97.7, respectively, for body line extraction. The precision, recall, and F1 score per document for the acute infection detection algorithm were 82.54 (95CI 72.86-91.60), 85.24 (95CI 76.61-93.70), 83.87 (95CI 76, 92-90.08) with exploitation of the results of the advanced body extraction algorithm, respectively. Conclusion:We have developed and validated a system for extracting body text from clinical documents in PDF format by identifying their layout. We were able to demonstrate that this preprocessing allowed us to obtain better performances for a common downstream task, i.e., the extraction of medical concepts in their respective sections, thus proving the interest of this method on a clinical use case.

  • 7 authors
·
May 23, 2023

MedTrinity-25M: A Large-scale Multimodal Dataset with Multigranular Annotations for Medicine

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

  • 11 authors
·
Aug 5, 2024 2

Multi-HMR: Multi-Person Whole-Body Human Mesh Recovery in a Single Shot

We present Multi-HMR, a strong sigle-shot model for multi-person 3D human mesh recovery from a single RGB image. Predictions encompass the whole body, i.e., including hands and facial expressions, using the SMPL-X parametric model and 3D location in the camera coordinate system. Our model detects people by predicting coarse 2D heatmaps of person locations, using features produced by a standard Vision Transformer (ViT) backbone. It then predicts their whole-body pose, shape and 3D location using a new cross-attention module called the Human Prediction Head (HPH), with one query attending to the entire set of features for each detected person. As direct prediction of fine-grained hands and facial poses in a single shot, i.e., without relying on explicit crops around body parts, is hard to learn from existing data, we introduce CUFFS, the Close-Up Frames of Full-Body Subjects dataset, containing humans close to the camera with diverse hand poses. We show that incorporating it into the training data further enhances predictions, particularly for hands. Multi-HMR also optionally accounts for camera intrinsics, if available, by encoding camera ray directions for each image token. This simple design achieves strong performance on whole-body and body-only benchmarks simultaneously: a ViT-S backbone on 448{times}448 images already yields a fast and competitive model, while larger models and higher resolutions obtain state-of-the-art results.

  • 7 authors
·
Feb 22, 2024

Recovering 3D Human Mesh from Monocular Images: A Survey

Estimating human pose and shape from monocular images is a long-standing problem in computer vision. Since the release of statistical body models, 3D human mesh recovery has been drawing broader attention. With the same goal of obtaining well-aligned and physically plausible mesh results, two paradigms have been developed to overcome challenges in the 2D-to-3D lifting process: i) an optimization-based paradigm, where different data terms and regularization terms are exploited as optimization objectives; and ii) a regression-based paradigm, where deep learning techniques are embraced to solve the problem in an end-to-end fashion. Meanwhile, continuous efforts are devoted to improving the quality of 3D mesh labels for a wide range of datasets. Though remarkable progress has been achieved in the past decade, the task is still challenging due to flexible body motions, diverse appearances, complex environments, and insufficient in-the-wild annotations. To the best of our knowledge, this is the first survey to focus on the task of monocular 3D human mesh recovery. We start with the introduction of body models and then elaborate recovery frameworks and training objectives by providing in-depth analyses of their strengths and weaknesses. We also summarize datasets, evaluation metrics, and benchmark results. Open issues and future directions are discussed in the end, hoping to motivate researchers and facilitate their research in this area. A regularly updated project page can be found at https://github.com/tinatiansjz/hmr-survey.

  • 4 authors
·
Mar 3, 2022

Generative Action Description Prompts for Skeleton-based Action Recognition

Skeleton-based action recognition has recently received considerable attention. Current approaches to skeleton-based action recognition are typically formulated as one-hot classification tasks and do not fully exploit the semantic relations between actions. For example, "make victory sign" and "thumb up" are two actions of hand gestures, whose major difference lies in the movement of hands. This information is agnostic from the categorical one-hot encoding of action classes but could be unveiled from the action description. Therefore, utilizing action description in training could potentially benefit representation learning. In this work, we propose a Generative Action-description Prompts (GAP) approach for skeleton-based action recognition. More specifically, we employ a pre-trained large-scale language model as the knowledge engine to automatically generate text descriptions for body parts movements of actions, and propose a multi-modal training scheme by utilizing the text encoder to generate feature vectors for different body parts and supervise the skeleton encoder for action representation learning. Experiments show that our proposed GAP method achieves noticeable improvements over various baseline models without extra computation cost at inference. GAP achieves new state-of-the-arts on popular skeleton-based action recognition benchmarks, including NTU RGB+D, NTU RGB+D 120 and NW-UCLA. The source code is available at https://github.com/MartinXM/GAP.

  • 5 authors
·
Aug 10, 2022

Embodied Hands: Modeling and Capturing Hands and Bodies Together

Humans move their hands and bodies together to communicate and solve tasks. Capturing and replicating such coordinated activity is critical for virtual characters that behave realistically. Surprisingly, most methods treat the 3D modeling and tracking of bodies and hands separately. Here we formulate a model of hands and bodies interacting together and fit it to full-body 4D sequences. When scanning or capturing the full body in 3D, hands are small and often partially occluded, making their shape and pose hard to recover. To cope with low-resolution, occlusion, and noise, we develop a new model called MANO (hand Model with Articulated and Non-rigid defOrmations). MANO is learned from around 1000 high-resolution 3D scans of hands of 31 subjects in a wide variety of hand poses. The model is realistic, low-dimensional, captures non-rigid shape changes with pose, is compatible with standard graphics packages, and can fit any human hand. MANO provides a compact mapping from hand poses to pose blend shape corrections and a linear manifold of pose synergies. We attach MANO to a standard parameterized 3D body shape model (SMPL), resulting in a fully articulated body and hand model (SMPL+H). We illustrate SMPL+H by fitting complex, natural, activities of subjects captured with a 4D scanner. The fitting is fully automatic and results in full body models that move naturally with detailed hand motions and a realism not seen before in full body performance capture. The models and data are freely available for research purposes in our website (http://mano.is.tue.mpg.de).

  • 3 authors
·
Jan 7, 2022

BiPO: Bidirectional Partial Occlusion Network for Text-to-Motion Synthesis

Generating natural and expressive human motions from textual descriptions is challenging due to the complexity of coordinating full-body dynamics and capturing nuanced motion patterns over extended sequences that accurately reflect the given text. To address this, we introduce BiPO, Bidirectional Partial Occlusion Network for Text-to-Motion Synthesis, a novel model that enhances text-to-motion synthesis by integrating part-based generation with a bidirectional autoregressive architecture. This integration allows BiPO to consider both past and future contexts during generation while enhancing detailed control over individual body parts without requiring ground-truth motion length. To relax the interdependency among body parts caused by the integration, we devise the Partial Occlusion technique, which probabilistically occludes the certain motion part information during training. In our comprehensive experiments, BiPO achieves state-of-the-art performance on the HumanML3D dataset, outperforming recent methods such as ParCo, MoMask, and BAMM in terms of FID scores and overall motion quality. Notably, BiPO excels not only in the text-to-motion generation task but also in motion editing tasks that synthesize motion based on partially generated motion sequences and textual descriptions. These results reveal the BiPO's effectiveness in advancing text-to-motion synthesis and its potential for practical applications.

  • 5 authors
·
Nov 28, 2024

The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT

This paper presents the challenge report for the 2021 Kidney and Kidney Tumor Segmentation Challenge (KiTS21) held in conjunction with the 2021 international conference on Medical Image Computing and Computer Assisted Interventions (MICCAI). KiTS21 is a sequel to its first edition in 2019, and it features a variety of innovations in how the challenge was designed, in addition to a larger dataset. A novel annotation method was used to collect three separate annotations for each region of interest, and these annotations were performed in a fully transparent setting using a web-based annotation tool. Further, the KiTS21 test set was collected from an outside institution, challenging participants to develop methods that generalize well to new populations. Nonetheless, the top-performing teams achieved a significant improvement over the state of the art set in 2019, and this performance is shown to inch ever closer to human-level performance. An in-depth meta-analysis is presented describing which methods were used and how they faired on the leaderboard, as well as the characteristics of which cases generally saw good performance, and which did not. Overall KiTS21 facilitated a significant advancement in the state of the art in kidney tumor segmentation, and provides useful insights that are applicable to the field of semantic segmentation as a whole.

  • 45 authors
·
Jul 4, 2023

PSUMNet: Unified Modality Part Streams are All You Need for Efficient Pose-based Action Recognition

Pose-based action recognition is predominantly tackled by approaches which treat the input skeleton in a monolithic fashion, i.e. joints in the pose tree are processed as a whole. However, such approaches ignore the fact that action categories are often characterized by localized action dynamics involving only small subsets of part joint groups involving hands (e.g. `Thumbs up') or legs (e.g. `Kicking'). Although part-grouping based approaches exist, each part group is not considered within the global pose frame, causing such methods to fall short. Further, conventional approaches employ independent modality streams (e.g. joint, bone, joint velocity, bone velocity) and train their network multiple times on these streams, which massively increases the number of training parameters. To address these issues, we introduce PSUMNet, a novel approach for scalable and efficient pose-based action recognition. At the representation level, we propose a global frame based part stream approach as opposed to conventional modality based streams. Within each part stream, the associated data from multiple modalities is unified and consumed by the processing pipeline. Experimentally, PSUMNet achieves state of the art performance on the widely used NTURGB+D 60/120 dataset and dense joint skeleton dataset NTU 60-X/120-X. PSUMNet is highly efficient and outperforms competing methods which use 100%-400% more parameters. PSUMNet also generalizes to the SHREC hand gesture dataset with competitive performance. Overall, PSUMNet's scalability, performance and efficiency makes it an attractive choice for action recognition and for deployment on compute-restricted embedded and edge devices. Code and pretrained models can be accessed at https://github.com/skelemoa/psumnet

  • 2 authors
·
Aug 11, 2022

SG-GS: Photo-realistic Animatable Human Avatars with Semantically-Guided Gaussian Splatting

Reconstructing photo-realistic animatable human avatars from monocular videos remains challenging in computer vision and graphics. Recently, methods using 3D Gaussians to represent the human body have emerged, offering faster optimization and real-time rendering. However, due to ignoring the crucial role of human body semantic information which represents the intrinsic structure and connections within the human body, they fail to achieve fine-detail reconstruction of dynamic human avatars. To address this issue, we propose SG-GS, which uses semantics-embedded 3D Gaussians, skeleton-driven rigid deformation, and non-rigid cloth dynamics deformation to create photo-realistic animatable human avatars from monocular videos. We then design a Semantic Human-Body Annotator (SHA) which utilizes SMPL's semantic prior for efficient body part semantic labeling. The generated labels are used to guide the optimization of Gaussian semantic attributes. To address the limited receptive field of point-level MLPs for local features, we also propose a 3D network that integrates geometric and semantic associations for human avatar deformation. We further implement three key strategies to enhance the semantic accuracy of 3D Gaussians and rendering quality: semantic projection with 2D regularization, semantic-guided density regularization and semantic-aware regularization with neighborhood consistency. Extensive experiments demonstrate that SG-GS achieves state-of-the-art geometry and appearance reconstruction performance.

  • 5 authors
·
Aug 18, 2024

Chest ImaGenome Dataset for Clinical Reasoning

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

  • 12 authors
·
Jul 31, 2021

Learning 3D Human Shape and Pose from Dense Body Parts

Reconstructing 3D human shape and pose from monocular images is challenging despite the promising results achieved by the most recent learning-based methods. The commonly occurred misalignment comes from the facts that the mapping from images to the model space is highly non-linear and the rotation-based pose representation of body models is prone to result in the drift of joint positions. In this work, we investigate learning 3D human shape and pose from dense correspondences of body parts and propose a Decompose-and-aggregate Network (DaNet) to address these issues. DaNet adopts the dense correspondence maps, which densely build a bridge between 2D pixels and 3D vertices, as intermediate representations to facilitate the learning of 2D-to-3D mapping. The prediction modules of DaNet are decomposed into one global stream and multiple local streams to enable global and fine-grained perceptions for the shape and pose predictions, respectively. Messages from local streams are further aggregated to enhance the robust prediction of the rotation-based poses, where a position-aided rotation feature refinement strategy is proposed to exploit spatial relationships between body joints. Moreover, a Part-based Dropout (PartDrop) strategy is introduced to drop out dense information from intermediate representations during training, encouraging the network to focus on more complementary body parts as well as neighboring position features. The efficacy of the proposed method is validated on both indoor and real-world datasets including Human3.6M, UP3D, COCO, and 3DPW, showing that our method could significantly improve the reconstruction performance in comparison with previous state-of-the-art methods. Our code is publicly available at https://hongwenzhang.github.io/dense2mesh .

  • 5 authors
·
Dec 31, 2019

Self-supervised Learning of Implicit Shape Representation with Dense Correspondence for Deformable Objects

Learning 3D shape representation with dense correspondence for deformable objects is a fundamental problem in computer vision. Existing approaches often need additional annotations of specific semantic domain, e.g., skeleton poses for human bodies or animals, which require extra annotation effort and suffer from error accumulation, and they are limited to specific domain. In this paper, we propose a novel self-supervised approach to learn neural implicit shape representation for deformable objects, which can represent shapes with a template shape and dense correspondence in 3D. Our method does not require the priors of skeleton and skinning weight, and only requires a collection of shapes represented in signed distance fields. To handle the large deformation, we constrain the learned template shape in the same latent space with the training shapes, design a new formulation of local rigid constraint that enforces rigid transformation in local region and addresses local reflection issue, and present a new hierarchical rigid constraint to reduce the ambiguity due to the joint learning of template shape and correspondences. Extensive experiments show that our model can represent shapes with large deformations. We also show that our shape representation can support two typical applications, such as texture transfer and shape editing, with competitive performance. The code and models are available at https://iscas3dv.github.io/deformshape

  • 6 authors
·
Aug 24, 2023

FineBio: A Fine-Grained Video Dataset of Biological Experiments with Hierarchical Annotation

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

  • 7 authors
·
Jan 31, 2024

BEDLAM: A Synthetic Dataset of Bodies Exhibiting Detailed Lifelike Animated Motion

We show, for the first time, that neural networks trained only on synthetic data achieve state-of-the-art accuracy on the problem of 3D human pose and shape (HPS) estimation from real images. Previous synthetic datasets have been small, unrealistic, or lacked realistic clothing. Achieving sufficient realism is non-trivial and we show how to do this for full bodies in motion. Specifically, our BEDLAM dataset contains monocular RGB videos with ground-truth 3D bodies in SMPL-X format. It includes a diversity of body shapes, motions, skin tones, hair, and clothing. The clothing is realistically simulated on the moving bodies using commercial clothing physics simulation. We render varying numbers of people in realistic scenes with varied lighting and camera motions. We then train various HPS regressors using BEDLAM and achieve state-of-the-art accuracy on real-image benchmarks despite training with synthetic data. We use BEDLAM to gain insights into what model design choices are important for accuracy. With good synthetic training data, we find that a basic method like HMR approaches the accuracy of the current SOTA method (CLIFF). BEDLAM is useful for a variety of tasks and all images, ground truth bodies, 3D clothing, support code, and more are available for research purposes. Additionally, we provide detailed information about our synthetic data generation pipeline, enabling others to generate their own datasets. See the project page: https://bedlam.is.tue.mpg.de/.

  • 4 authors
·
Jun 29, 2023

FinePOSE: Fine-Grained Prompt-Driven 3D Human Pose Estimation via Diffusion Models

The 3D Human Pose Estimation (3D HPE) task uses 2D images or videos to predict human joint coordinates in 3D space. Despite recent advancements in deep learning-based methods, they mostly ignore the capability of coupling accessible texts and naturally feasible knowledge of humans, missing out on valuable implicit supervision to guide the 3D HPE task. Moreover, previous efforts often study this task from the perspective of the whole human body, neglecting fine-grained guidance hidden in different body parts. To this end, we present a new Fine-Grained Prompt-Driven Denoiser based on a diffusion model for 3D HPE, named FinePOSE. It consists of three core blocks enhancing the reverse process of the diffusion model: (1) Fine-grained Part-aware Prompt learning (FPP) block constructs fine-grained part-aware prompts via coupling accessible texts and naturally feasible knowledge of body parts with learnable prompts to model implicit guidance. (2) Fine-grained Prompt-pose Communication (FPC) block establishes fine-grained communications between learned part-aware prompts and poses to improve the denoising quality. (3) Prompt-driven Timestamp Stylization (PTS) block integrates learned prompt embedding and temporal information related to the noise level to enable adaptive adjustment at each denoising step. Extensive experiments on public single-human pose estimation datasets show that FinePOSE outperforms state-of-the-art methods. We further extend FinePOSE to multi-human pose estimation. Achieving 34.3mm average MPJPE on the EgoHumans dataset demonstrates the potential of FinePOSE to deal with complex multi-human scenarios. Code is available at https://github.com/PKU-ICST-MIPL/FinePOSE_CVPR2024.

  • 3 authors
·
May 8, 2024

Towards Measuring Fairness in AI: the Casual Conversations Dataset

This paper introduces a novel dataset to help researchers evaluate their computer vision and audio models for accuracy across a diverse set of age, genders, apparent skin tones and ambient lighting conditions. Our dataset is composed of 3,011 subjects and contains over 45,000 videos, with an average of 15 videos per person. The videos were recorded in multiple U.S. states with a diverse set of adults in various age, gender and apparent skin tone groups. A key feature is that each subject agreed to participate for their likenesses to be used. Additionally, our age and gender annotations are provided by the subjects themselves. A group of trained annotators labeled the subjects' apparent skin tone using the Fitzpatrick skin type scale. Moreover, annotations for videos recorded in low ambient lighting are also provided. As an application to measure robustness of predictions across certain attributes, we provide a comprehensive study on the top five winners of the DeepFake Detection Challenge (DFDC). Experimental evaluation shows that the winning models are less performant on some specific groups of people, such as subjects with darker skin tones and thus may not generalize to all people. In addition, we also evaluate the state-of-the-art apparent age and gender classification methods. Our experiments provides a thorough analysis on these models in terms of fair treatment of people from various backgrounds.

  • 6 authors
·
Apr 6, 2021

BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

  • 16 authors
·
Jan 13 3

Biomed-Enriched: A Biomedical Dataset Enriched with LLMs for Pretraining and Extracting Rare and Hidden Content

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

  • 3 authors
·
Jun 25 1

Deep Fashion3D: A Dataset and Benchmark for 3D Garment Reconstruction from Single Images

High-fidelity clothing reconstruction is the key to achieving photorealism in a wide range of applications including human digitization, virtual try-on, etc. Recent advances in learning-based approaches have accomplished unprecedented accuracy in recovering unclothed human shape and pose from single images, thanks to the availability of powerful statistical models, e.g. SMPL, learned from a large number of body scans. In contrast, modeling and recovering clothed human and 3D garments remains notoriously difficult, mostly due to the lack of large-scale clothing models available for the research community. We propose to fill this gap by introducing Deep Fashion3D, the largest collection to date of 3D garment models, with the goal of establishing a novel benchmark and dataset for the evaluation of image-based garment reconstruction systems. Deep Fashion3D contains 2078 models reconstructed from real garments, which covers 10 different categories and 563 garment instances. It provides rich annotations including 3D feature lines, 3D body pose and the corresponded multi-view real images. In addition, each garment is randomly posed to enhance the variety of real clothing deformations. To demonstrate the advantage of Deep Fashion3D, we propose a novel baseline approach for single-view garment reconstruction, which leverages the merits of both mesh and implicit representations. A novel adaptable template is proposed to enable the learning of all types of clothing in a single network. Extensive experiments have been conducted on the proposed dataset to verify its significance and usefulness. We will make Deep Fashion3D publicly available upon publication.

  • 8 authors
·
Mar 28, 2020

One Model to Rule them All: Towards Universal Segmentation for Medical Images with Text Prompts

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

  • 7 authors
·
Dec 28, 2023

PyMAF-X: Towards Well-aligned Full-body Model Regression from Monocular Images

We present PyMAF-X, a regression-based approach to recovering parametric full-body models from monocular images. This task is very challenging since minor parametric deviation may lead to noticeable misalignment between the estimated mesh and the input image. Moreover, when integrating part-specific estimations into the full-body model, existing solutions tend to either degrade the alignment or produce unnatural wrist poses. To address these issues, we propose a Pyramidal Mesh Alignment Feedback (PyMAF) loop in our regression network for well-aligned human mesh recovery and extend it as PyMAF-X for the recovery of expressive full-body models. The core idea of PyMAF is to leverage a feature pyramid and rectify the predicted parameters explicitly based on the mesh-image alignment status. Specifically, given the currently predicted parameters, mesh-aligned evidence will be extracted from finer-resolution features accordingly and fed back for parameter rectification. To enhance the alignment perception, an auxiliary dense supervision is employed to provide mesh-image correspondence guidance while spatial alignment attention is introduced to enable the awareness of the global contexts for our network. When extending PyMAF for full-body mesh recovery, an adaptive integration strategy is proposed in PyMAF-X to produce natural wrist poses while maintaining the well-aligned performance of the part-specific estimations. The efficacy of our approach is validated on several benchmark datasets for body, hand, face, and full-body mesh recovery, where PyMAF and PyMAF-X effectively improve the mesh-image alignment and achieve new state-of-the-art results. The project page with code and video results can be found at https://www.liuyebin.com/pymaf-x.

  • 7 authors
·
Jul 13, 2022

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

  • 4 authors
·
Feb 28, 2022

Visual Genome: Connecting Language and Vision Using Crowdsourced Dense Image Annotations

Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) in order to answer correctly that "the person is riding a horse-drawn carriage". In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 100K images where each image has an average of 21 objects, 18 attributes, and 18 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answers.

  • 12 authors
·
Feb 23, 2016

HD-EPIC: A Highly-Detailed Egocentric Video Dataset

We present a validation dataset of newly-collected kitchen-based egocentric videos, manually annotated with highly detailed and interconnected ground-truth labels covering: recipe steps, fine-grained actions, ingredients with nutritional values, moving objects, and audio annotations. Importantly, all annotations are grounded in 3D through digital twinning of the scene, fixtures, object locations, and primed with gaze. Footage is collected from unscripted recordings in diverse home environments, making HDEPIC the first dataset collected in-the-wild but with detailed annotations matching those in controlled lab environments. We show the potential of our highly-detailed annotations through a challenging VQA benchmark of 26K questions assessing the capability to recognise recipes, ingredients, nutrition, fine-grained actions, 3D perception, object motion, and gaze direction. The powerful long-context Gemini Pro only achieves 38.5% on this benchmark, showcasing its difficulty and highlighting shortcomings in current VLMs. We additionally assess action recognition, sound recognition, and long-term video-object segmentation on HD-EPIC. HD-EPIC is 41 hours of video in 9 kitchens with digital twins of 413 kitchen fixtures, capturing 69 recipes, 59K fine-grained actions, 51K audio events, 20K object movements and 37K object masks lifted to 3D. On average, we have 263 annotations per minute of our unscripted videos.

  • 19 authors
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Feb 6

CholecTrack20: A Multi-Perspective Tracking Dataset for Surgical Tools

Tool tracking in surgical videos is essential for advancing computer-assisted interventions, such as skill assessment, safety zone estimation, and human-machine collaboration. However, the lack of context-rich datasets limits AI applications in this field. Existing datasets rely on overly generic tracking formalizations that fail to capture surgical-specific dynamics, such as tools moving out of the camera's view or exiting the body. This results in less clinically relevant trajectories and a lack of flexibility for real-world surgical applications. Methods trained on these datasets often struggle with visual challenges such as smoke, reflection, and bleeding, further exposing the limitations of current approaches. We introduce CholecTrack20, a specialized dataset for multi-class, multi-tool tracking in surgical procedures. It redefines tracking formalization with three perspectives: (i) intraoperative, (ii) intracorporeal, and (iii) visibility, enabling adaptable and clinically meaningful tool trajectories. The dataset comprises 20 full-length surgical videos, annotated at 1 fps, yielding over 35K frames and 65K labeled tool instances. Annotations include spatial location, category, identity, operator, phase, and scene visual challenge. Benchmarking state-of-the-art methods on CholecTrack20 reveals significant performance gaps, with current approaches (< 45\% HOTA) failing to meet the accuracy required for clinical translation. These findings motivate the need for advanced and intuitive tracking algorithms and establish CholecTrack20 as a foundation for developing robust AI-driven surgical assistance systems.

  • 6 authors
·
Dec 12, 2023

Learning 3D Texture-Aware Representations for Parsing Diverse Human Clothing and Body Parts

Existing methods for human parsing into body parts and clothing often use fixed mask categories with broad labels that obscure fine-grained clothing types. Recent open-vocabulary segmentation approaches leverage pretrained text-to-image (T2I) diffusion model features for strong zero-shot transfer, but typically group entire humans into a single person category, failing to distinguish diverse clothing or detailed body parts. To address this, we propose Spectrum, a unified network for part-level pixel parsing (body parts and clothing) and instance-level grouping. While diffusion-based open-vocabulary models generalize well across tasks, their internal representations are not specialized for detailed human parsing. We observe that, unlike diffusion models with broad representations, image-driven 3D texture generators maintain faithful correspondence to input images, enabling stronger representations for parsing diverse clothing and body parts. Spectrum introduces a novel repurposing of an Image-to-Texture (I2Tx) diffusion model -- obtained by fine-tuning a T2I model on 3D human texture maps -- for improved alignment with body parts and clothing. From an input image, we extract human-part internal features via the I2Tx diffusion model and generate semantically valid masks aligned to diverse clothing categories through prompt-guided grounding. Once trained, Spectrum produces semantic segmentation maps for every visible body part and clothing category, ignoring standalone garments or irrelevant objects, for any number of humans in the scene. We conduct extensive cross-dataset experiments -- separately assessing body parts, clothing parts, unseen clothing categories, and full-body masks -- and demonstrate that Spectrum consistently outperforms baseline methods in prompt-based segmentation.

  • 3 authors
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Aug 8

PostoMETRO: Pose Token Enhanced Mesh Transformer for Robust 3D Human Mesh Recovery

With the recent advancements in single-image-based human mesh recovery, there is a growing interest in enhancing its performance in certain extreme scenarios, such as occlusion, while maintaining overall model accuracy. Although obtaining accurately annotated 3D human poses under occlusion is challenging, there is still a wealth of rich and precise 2D pose annotations that can be leveraged. However, existing works mostly focus on directly leveraging 2D pose coordinates to estimate 3D pose and mesh. In this paper, we present PostoMETRO(Pose token enhanced MEsh TRansfOrmer), which integrates occlusion-resilient 2D pose representation into transformers in a token-wise manner. Utilizing a specialized pose tokenizer, we efficiently condense 2D pose data to a compact sequence of pose tokens and feed them to the transformer together with the image tokens. This process not only ensures a rich depiction of texture from the image but also fosters a robust integration of pose and image information. Subsequently, these combined tokens are queried by vertex and joint tokens to decode 3D coordinates of mesh vertices and human joints. Facilitated by the robust pose token representation and the effective combination, we are able to produce more precise 3D coordinates, even under extreme scenarios like occlusion. Experiments on both standard and occlusion-specific benchmarks demonstrate the effectiveness of PostoMETRO. Qualitative results further illustrate the clarity of how 2D pose can help 3D reconstruction. Code will be made available.

  • 4 authors
·
Mar 19, 2024

MedBookVQA: A Systematic and Comprehensive Medical Benchmark Derived from Open-Access Book

The accelerating development of general medical artificial intelligence (GMAI), powered by multimodal large language models (MLLMs), offers transformative potential for addressing persistent healthcare challenges, including workforce deficits and escalating costs. The parallel development of systematic evaluation benchmarks emerges as a critical imperative to enable performance assessment and provide technological guidance. Meanwhile, as an invaluable knowledge source, the potential of medical textbooks for benchmark development remains underexploited. Here, we present MedBookVQA, a systematic and comprehensive multimodal benchmark derived from open-access medical textbooks. To curate this benchmark, we propose a standardized pipeline for automated extraction of medical figures while contextually aligning them with corresponding medical narratives. Based on this curated data, we generate 5,000 clinically relevant questions spanning modality recognition, disease classification, anatomical identification, symptom diagnosis, and surgical procedures. A multi-tier annotation system categorizes queries through hierarchical taxonomies encompassing medical imaging modalities (42 categories), body anatomies (125 structures), and clinical specialties (31 departments), enabling nuanced analysis across medical subdomains. We evaluate a wide array of MLLMs, including proprietary, open-sourced, medical, and reasoning models, revealing significant performance disparities across task types and model categories. Our findings highlight critical capability gaps in current GMAI systems while establishing textbook-derived multimodal benchmarks as essential evaluation tools. MedBookVQA establishes textbook-derived benchmarking as a critical paradigm for advancing clinical AI, exposing limitations in GMAI systems while providing anatomically structured performance metrics across specialties.

  • 7 authors
·
Jun 1

Unsupervised domain adaptation for clinician pose estimation and instance segmentation in the operating room

The fine-grained localization of clinicians in the operating room (OR) is a key component to design the new generation of OR support systems. Computer vision models for person pixel-based segmentation and body-keypoints detection are needed to better understand the clinical activities and the spatial layout of the OR. This is challenging, not only because OR images are very different from traditional vision datasets, but also because data and annotations are hard to collect and generate in the OR due to privacy concerns. To address these concerns, we first study how joint person pose estimation and instance segmentation can be performed on low resolutions images with downsampling factors from 1x to 12x. Second, to address the domain shift and the lack of annotations, we propose a novel unsupervised domain adaptation method, called AdaptOR, to adapt a model from an in-the-wild labeled source domain to a statistically different unlabeled target domain. We propose to exploit explicit geometric constraints on the different augmentations of the unlabeled target domain image to generate accurate pseudo labels and use these pseudo labels to train the model on high- and low-resolution OR images in a self-training framework. Furthermore, we propose disentangled feature normalization to handle the statistically different source and target domain data. Extensive experimental results with detailed ablation studies on the two OR datasets MVOR+ and TUM-OR-test show the effectiveness of our approach against strongly constructed baselines, especially on the low-resolution privacy-preserving OR images. Finally, we show the generality of our method as a semi-supervised learning (SSL) method on the large-scale COCO dataset, where we achieve comparable results with as few as 1% of labeled supervision against a model trained with 100% labeled supervision.

  • 3 authors
·
Aug 26, 2021

Pose as Clinical Prior: Learning Dual Representations for Scoliosis Screening

Recent AI-based scoliosis screening methods primarily rely on large-scale silhouette datasets, often neglecting clinically relevant postural asymmetries-key indicators in traditional screening. In contrast, pose data provide an intuitive skeletal representation, enhancing clinical interpretability across various medical applications. However, pose-based scoliosis screening remains underexplored due to two main challenges: (1) the scarcity of large-scale, annotated pose datasets; and (2) the discrete and noise-sensitive nature of raw pose coordinates, which hinders the modeling of subtle asymmetries. To address these limitations, we introduce Scoliosis1K-Pose, a 2D human pose annotation set that extends the original Scoliosis1K dataset, comprising 447,900 frames of 2D keypoints from 1,050 adolescents. Building on this dataset, we introduce the Dual Representation Framework (DRF), which integrates a continuous skeleton map to preserve spatial structure with a discrete Postural Asymmetry Vector (PAV) that encodes clinically relevant asymmetry descriptors. A novel PAV-Guided Attention (PGA) module further uses the PAV as clinical prior to direct feature extraction from the skeleton map, focusing on clinically meaningful asymmetries. Extensive experiments demonstrate that DRF achieves state-of-the-art performance. Visualizations further confirm that the model leverages clinical asymmetry cues to guide feature extraction and promote synergy between its dual representations. The dataset and code are publicly available at https://zhouzi180.github.io/Scoliosis1K/.

  • 6 authors
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Aug 31

nnLandmark: A Self-Configuring Method for 3D Medical Landmark Detection

Landmark detection plays a crucial role in medical imaging tasks that rely on precise spatial localization, including specific applications in diagnosis, treatment planning, image registration, and surgical navigation. However, manual annotation is labor-intensive and requires expert knowledge. While deep learning shows promise in automating this task, progress is hindered by limited public datasets, inconsistent benchmarks, and non-standardized baselines, restricting reproducibility, fair comparisons, and model generalizability. This work introduces nnLandmark, a self-configuring deep learning framework for 3D medical landmark detection, adapting nnU-Net to perform heatmap-based regression. By leveraging nnU-Net's automated configuration, nnLandmark eliminates the need for manual parameter tuning, offering out-of-the-box usability. It achieves state-of-the-art accuracy across two public datasets, with a mean radial error (MRE) of 1.5 mm on the Mandibular Molar Landmark (MML) dental CT dataset and 1.2 mm for anatomical fiducials on a brain MRI dataset (AFIDs), where nnLandmark aligns with the inter-rater variability of 1.5 mm. With its strong generalization, reproducibility, and ease of deployment, nnLandmark establishes a reliable baseline for 3D landmark detection, supporting research in anatomical localization and clinical workflows that depend on precise landmark identification. The code will be available soon.

  • 8 authors
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Apr 9

PARTONOMY: Large Multimodal Models with Part-Level Visual Understanding

Real-world objects are composed of distinctive, object-specific parts. Identifying these parts is key to performing fine-grained, compositional reasoning-yet, large multimodal models (LMMs) struggle to perform this seemingly straightforward task. In this work, we introduce PARTONOMY, an LMM benchmark designed for pixel-level part grounding. We construct PARTONOMY from existing part datasets and our own rigorously annotated set of images, encompassing 862 part labels and 534 object labels for evaluation. Unlike existing datasets that simply ask models to identify generic parts, PARTONOMY uses specialized concepts (e.g., agricultural airplane), and challenges models to compare objects' parts, consider part-whole relationships, and justify textual predictions with visual segmentations. Our experiments demonstrate significant limitations in state-of-the-art LMMs (e.g., LISA-13B achieves only 5.9% gIoU), highlighting a critical gap in their part grounding abilities. We note that existing segmentation-enabled LMMs (segmenting LMMs) have two key architectural shortcomings: they use special [SEG] tokens not seen during pretraining which induce distribution shift, and they discard predicted segmentations instead of using past predictions to guide future ones. To address these deficiencies, we train several part-centric LMMs and propose PLUM, a novel segmenting LMM that uses span tagging instead of segmentation tokens and that conditions on prior predictions in a feedback loop. We find that pretrained PLUM outperforms existing segmenting LMMs on reasoning segmentation, VQA, and visual hallucination benchmarks. In addition, PLUM finetuned on our proposed Explanatory Part Segmentation task is competitive with segmenting LMMs trained on significantly more segmentation data. Our work opens up new avenues towards enabling fine-grained, grounded visual understanding in LMMs.

  • 10 authors
·
May 27

NuClick: A Deep Learning Framework for Interactive Segmentation of Microscopy Images

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

  • 4 authors
·
May 29, 2020

Computer vision for liquid samples in hospitals and medical labs using hierarchical image segmentation and relations prediction

This work explores the use of computer vision for image segmentation and classification of medical fluid samples in transparent containers (for example, tubes, syringes, infusion bags). Handling fluids such as infusion fluids, blood, and urine samples is a significant part of the work carried out in medical labs and hospitals. The ability to accurately identify and segment the liquids and the vessels that contain them from images can help in automating such processes. Modern computer vision typically involves training deep neural nets on large datasets of annotated images. This work presents a new dataset containing 1,300 annotated images of medical samples involving vessels containing liquids and solid material. The images are annotated with the type of liquid (e.g., blood, urine), the phase of the material (e.g., liquid, solid, foam, suspension), the type of vessel (e.g., syringe, tube, cup, infusion bottle/bag), and the properties of the vessel (transparent, opaque). In addition, vessel parts such as corks, labels, spikes, and valves are annotated. Relations and hierarchies between vessels and materials are also annotated, such as which vessel contains which material or which vessels are linked or contain each other. Three neural networks are trained on the dataset: One network learns to detect vessels, a second net detects the materials and parts inside each vessel, and a third net identifies relationships and connectivity between vessels.

  • 3 authors
·
May 4, 2021

UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image Segmentation

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.