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Nov 6

NeRF-based Point Cloud Reconstruction using a Stationary Camera for Agricultural Applications

This paper presents a NeRF-based framework for point cloud (PCD) reconstruction, specifically designed for indoor high-throughput plant phenotyping facilities. Traditional NeRF-based reconstruction methods require cameras to move around stationary objects, but this approach is impractical for high-throughput environments where objects are rapidly imaged while moving on conveyors or rotating pedestals. To address this limitation, we develop a variant of NeRF-based PCD reconstruction that uses a single stationary camera to capture images as the object rotates on a pedestal. Our workflow comprises COLMAP-based pose estimation, a straightforward pose transformation to simulate camera movement, and subsequent standard NeRF training. A defined Region of Interest (ROI) excludes irrelevant scene data, enabling the generation of high-resolution point clouds (10M points). Experimental results demonstrate excellent reconstruction fidelity, with precision-recall analyses yielding an F-score close to 100.00 across all evaluated plant objects. Although pose estimation remains computationally intensive with a stationary camera setup, overall training and reconstruction times are competitive, validating the method's feasibility for practical high-throughput indoor phenotyping applications. Our findings indicate that high-quality NeRF-based 3D reconstructions are achievable using a stationary camera, eliminating the need for complex camera motion or costly imaging equipment. This approach is especially beneficial when employing expensive and delicate instruments, such as hyperspectral cameras, for 3D plant phenotyping. Future work will focus on optimizing pose estimation techniques and further streamlining the methodology to facilitate seamless integration into automated, high-throughput 3D phenotyping pipelines.

  • 7 authors
·
Mar 27

A General-Purpose Self-Supervised Model for Computational Pathology

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

  • 20 authors
·
Aug 29, 2023

Beyond the Pixel: a Photometrically Calibrated HDR Dataset for Luminance and Color Prediction

Light plays an important role in human well-being. However, most computer vision tasks treat pixels without considering their relationship to physical luminance. To address this shortcoming, we introduce the Laval Photometric Indoor HDR Dataset, the first large-scale photometrically calibrated dataset of high dynamic range 360{\deg} panoramas. Our key contribution is the calibration of an existing, uncalibrated HDR Dataset. We do so by accurately capturing RAW bracketed exposures simultaneously with a professional photometric measurement device (chroma meter) for multiple scenes across a variety of lighting conditions. Using the resulting measurements, we establish the calibration coefficients to be applied to the HDR images. The resulting dataset is a rich representation of indoor scenes which displays a wide range of illuminance and color, and varied types of light sources. We exploit the dataset to introduce three novel tasks, where: per-pixel luminance, per-pixel color and planar illuminance can be predicted from a single input image. Finally, we also capture another smaller photometric dataset with a commercial 360{\deg} camera, to experiment on generalization across cameras. We are optimistic that the release of our datasets and associated code will spark interest in physically accurate light estimation within the community. Dataset and code are available at https://lvsn.github.io/beyondthepixel/.

  • 5 authors
·
Apr 24, 2023

A Corpus for Detecting High-Context Medical Conditions in Intensive Care Patient Notes Focusing on Frequently Readmitted Patients

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

  • 10 authors
·
Mar 6, 2020

ROOM: A Physics-Based Continuum Robot Simulator for Photorealistic Medical Datasets Generation

Continuum robots are advancing bronchoscopy procedures by accessing complex lung airways and enabling targeted interventions. However, their development is limited by the lack of realistic training and test environments: Real data is difficult to collect due to ethical constraints and patient safety concerns, and developing autonomy algorithms requires realistic imaging and physical feedback. We present ROOM (Realistic Optical Observation in Medicine), a comprehensive simulation framework designed for generating photorealistic bronchoscopy training data. By leveraging patient CT scans, our pipeline renders multi-modal sensor data including RGB images with realistic noise and light specularities, metric depth maps, surface normals, optical flow and point clouds at medically relevant scales. We validate the data generated by ROOM in two canonical tasks for medical robotics -- multi-view pose estimation and monocular depth estimation, demonstrating diverse challenges that state-of-the-art methods must overcome to transfer to these medical settings. Furthermore, we show that the data produced by ROOM can be used to fine-tune existing depth estimation models to overcome these challenges, also enabling other downstream applications such as navigation. We expect that ROOM will enable large-scale data generation across diverse patient anatomies and procedural scenarios that are challenging to capture in clinical settings. Code and data: https://github.com/iamsalvatore/room.

  • 7 authors
·
Sep 16 2

ROOT: VLM based System for Indoor Scene Understanding and Beyond

Recently, Vision Language Models (VLMs) have experienced significant advancements, yet these models still face challenges in spatial hierarchical reasoning within indoor scenes. In this study, we introduce ROOT, a VLM-based system designed to enhance the analysis of indoor scenes. Specifically, we first develop an iterative object perception algorithm using GPT-4V to detect object entities within indoor scenes. This is followed by employing vision foundation models to acquire additional meta-information about the scene, such as bounding boxes. Building on this foundational data, we propose a specialized VLM, SceneVLM, which is capable of generating spatial hierarchical scene graphs and providing distance information for objects within indoor environments. This information enhances our understanding of the spatial arrangement of indoor scenes. To train our SceneVLM, we collect over 610,000 images from various public indoor datasets and implement a scene data generation pipeline with a semi-automated technique to establish relationships and estimate distances among indoor objects. By utilizing this enriched data, we conduct various training recipes and finish SceneVLM. Our experiments demonstrate that \rootname facilitates indoor scene understanding and proves effective in diverse downstream applications, such as 3D scene generation and embodied AI. The code will be released at https://github.com/harrytea/ROOT.

  • 7 authors
·
Nov 23, 2024

ReSpace: Text-Driven 3D Scene Synthesis and Editing with Preference Alignment

Scene synthesis and editing has emerged as a promising direction in computer graphics. Current trained approaches for 3D indoor scenes either oversimplify object semantics through one-hot class encodings (e.g., 'chair' or 'table'), require masked diffusion for editing, ignore room boundaries, or rely on floor plan renderings that fail to capture complex layouts. In contrast, LLM-based methods enable richer semantics via natural language (e.g., 'modern studio with light wood furniture') but do not support editing, remain limited to rectangular layouts or rely on weak spatial reasoning from implicit world models. We introduce ReSpace, a generative framework for text-driven 3D indoor scene synthesis and editing using autoregressive language models. Our approach features a compact structured scene representation with explicit room boundaries that frames scene editing as a next-token prediction task. We leverage a dual-stage training approach combining supervised fine-tuning and preference alignment, enabling a specially trained language model for object addition that accounts for user instructions, spatial geometry, object semantics, and scene-level composition. For scene editing, we employ a zero-shot LLM to handle object removal and prompts for addition. We further introduce a novel voxelization-based evaluation that captures fine-grained geometry beyond 3D bounding boxes. Experimental results surpass state-of-the-art on object addition while maintaining competitive results on full scene synthesis.

  • 2 authors
·
Jun 3

Indoor Scene Generation from a Collection of Semantic-Segmented Depth Images

We present a method for creating 3D indoor scenes with a generative model learned from a collection of semantic-segmented depth images captured from different unknown scenes. Given a room with a specified size, our method automatically generates 3D objects in a room from a randomly sampled latent code. Different from existing methods that represent an indoor scene with the type, location, and other properties of objects in the room and learn the scene layout from a collection of complete 3D indoor scenes, our method models each indoor scene as a 3D semantic scene volume and learns a volumetric generative adversarial network (GAN) from a collection of 2.5D partial observations of 3D scenes. To this end, we apply a differentiable projection layer to project the generated 3D semantic scene volumes into semantic-segmented depth images and design a new multiple-view discriminator for learning the complete 3D scene volume from 2.5D semantic-segmented depth images. Compared to existing methods, our method not only efficiently reduces the workload of modeling and acquiring 3D scenes for training, but also produces better object shapes and their detailed layouts in the scene. We evaluate our method with different indoor scene datasets and demonstrate the advantages of our method. We also extend our method for generating 3D indoor scenes from semantic-segmented depth images inferred from RGB images of real scenes.

  • 4 authors
·
Aug 20, 2021

SceneHGN: Hierarchical Graph Networks for 3D Indoor Scene Generation with Fine-Grained Geometry

3D indoor scenes are widely used in computer graphics, with applications ranging from interior design to gaming to virtual and augmented reality. They also contain rich information, including room layout, as well as furniture type, geometry, and placement. High-quality 3D indoor scenes are highly demanded while it requires expertise and is time-consuming to design high-quality 3D indoor scenes manually. Existing research only addresses partial problems: some works learn to generate room layout, and other works focus on generating detailed structure and geometry of individual furniture objects. However, these partial steps are related and should be addressed together for optimal synthesis. We propose SCENEHGN, a hierarchical graph network for 3D indoor scenes that takes into account the full hierarchy from the room level to the object level, then finally to the object part level. Therefore for the first time, our method is able to directly generate plausible 3D room content, including furniture objects with fine-grained geometry, and their layout. To address the challenge, we introduce functional regions as intermediate proxies between the room and object levels to make learning more manageable. To ensure plausibility, our graph-based representation incorporates both vertical edges connecting child nodes with parent nodes from different levels, and horizontal edges encoding relationships between nodes at the same level. Extensive experiments demonstrate that our method produces superior generation results, even when comparing results of partial steps with alternative methods that can only achieve these. We also demonstrate that our method is effective for various applications such as part-level room editing, room interpolation, and room generation by arbitrary room boundaries.

  • 6 authors
·
Feb 16, 2023

Experimental Design for Multi-Channel Imaging via Task-Driven Feature Selection

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

  • 3 authors
·
Oct 13, 2022

Cubify Anything: Scaling Indoor 3D Object Detection

We consider indoor 3D object detection with respect to a single RGB(-D) frame acquired from a commodity handheld device. We seek to significantly advance the status quo with respect to both data and modeling. First, we establish that existing datasets have significant limitations to scale, accuracy, and diversity of objects. As a result, we introduce the Cubify-Anything 1M (CA-1M) dataset, which exhaustively labels over 400K 3D objects on over 1K highly accurate laser-scanned scenes with near-perfect registration to over 3.5K handheld, egocentric captures. Next, we establish Cubify Transformer (CuTR), a fully Transformer 3D object detection baseline which rather than operating in 3D on point or voxel-based representations, predicts 3D boxes directly from 2D features derived from RGB(-D) inputs. While this approach lacks any 3D inductive biases, we show that paired with CA-1M, CuTR outperforms point-based methods - accurately recalling over 62% of objects in 3D, and is significantly more capable at handling noise and uncertainty present in commodity LiDAR-derived depth maps while also providing promising RGB only performance without architecture changes. Furthermore, by pre-training on CA-1M, CuTR can outperform point-based methods on a more diverse variant of SUN RGB-D - supporting the notion that while inductive biases in 3D are useful at the smaller sizes of existing datasets, they fail to scale to the data-rich regime of CA-1M. Overall, this dataset and baseline model provide strong evidence that we are moving towards models which can effectively Cubify Anything.

  • 5 authors
·
Dec 5, 2024

EPFL-Smart-Kitchen-30: Densely annotated cooking dataset with 3D kinematics to challenge video and language models

Understanding behavior requires datasets that capture humans while carrying out complex tasks. The kitchen is an excellent environment for assessing human motor and cognitive function, as many complex actions are naturally exhibited in kitchens from chopping to cleaning. Here, we introduce the EPFL-Smart-Kitchen-30 dataset, collected in a noninvasive motion capture platform inside a kitchen environment. Nine static RGB-D cameras, inertial measurement units (IMUs) and one head-mounted HoloLens~2 headset were used to capture 3D hand, body, and eye movements. The EPFL-Smart-Kitchen-30 dataset is a multi-view action dataset with synchronized exocentric, egocentric, depth, IMUs, eye gaze, body and hand kinematics spanning 29.7 hours of 16 subjects cooking four different recipes. Action sequences were densely annotated with 33.78 action segments per minute. Leveraging this multi-modal dataset, we propose four benchmarks to advance behavior understanding and modeling through 1) a vision-language benchmark, 2) a semantic text-to-motion generation benchmark, 3) a multi-modal action recognition benchmark, 4) a pose-based action segmentation benchmark. We expect the EPFL-Smart-Kitchen-30 dataset to pave the way for better methods as well as insights to understand the nature of ecologically-valid human behavior. Code and data are available at https://github.com/amathislab/EPFL-Smart-Kitchen

  • 10 authors
·
Jun 2

Prototype Learning to Create Refined Interpretable Digital Phenotypes from ECGs

Prototype-based neural networks offer interpretable predictions by comparing inputs to learned, representative signal patterns anchored in training data. While such models have shown promise in the classification of physiological data, it remains unclear whether their prototypes capture an underlying structure that aligns with broader clinical phenotypes. We use a prototype-based deep learning model trained for multi-label ECG classification using the PTB-XL dataset. Then without modification we performed inference on the MIMIC-IV clinical database. We assess whether individual prototypes, trained solely for classification, are associated with hospital discharge diagnoses in the form of phecodes in this external population. Individual prototypes demonstrate significantly stronger and more specific associations with clinical outcomes compared to the classifier's class predictions, NLP-extracted concepts, or broader prototype classes across all phecode categories. Prototype classes with mixed significance patterns exhibit significantly greater intra-class distances (p < 0.0001), indicating the model learned to differentiate clinically meaningful variations within diagnostic categories. The prototypes achieve strong predictive performance across diverse conditions, with AUCs ranging from 0.89 for atrial fibrillation to 0.91 for heart failure, while also showing substantial signal for non-cardiac conditions such as sepsis and renal disease. These findings suggest that prototype-based models can support interpretable digital phenotyping from physiologic time-series data, providing transferable intermediate phenotypes that capture clinically meaningful physiologic signatures beyond their original training objectives.

  • 6 authors
·
Aug 2

Style-Consistent 3D Indoor Scene Synthesis with Decoupled Objects

Controllable 3D indoor scene synthesis stands at the forefront of technological progress, offering various applications like gaming, film, and augmented/virtual reality. The capability to stylize and de-couple objects within these scenarios is a crucial factor, providing an advanced level of control throughout the editing process. This control extends not just to manipulating geometric attributes like translation and scaling but also includes managing appearances, such as stylization. Current methods for scene stylization are limited to applying styles to the entire scene, without the ability to separate and customize individual objects. Addressing the intricacies of this challenge, we introduce a unique pipeline designed for synthesis 3D indoor scenes. Our approach involves strategically placing objects within the scene, utilizing information from professionally designed bounding boxes. Significantly, our pipeline prioritizes maintaining style consistency across multiple objects within the scene, ensuring a cohesive and visually appealing result aligned with the desired aesthetic. The core strength of our pipeline lies in its ability to generate 3D scenes that are not only visually impressive but also exhibit features like photorealism, multi-view consistency, and diversity. These scenes are crafted in response to various natural language prompts, demonstrating the versatility and adaptability of our model.

  • 7 authors
·
Jan 23, 2024

AI Playground: Unreal Engine-based Data Ablation Tool for Deep Learning

Machine learning requires data, but acquiring and labeling real-world data is challenging, expensive, and time-consuming. More importantly, it is nearly impossible to alter real data post-acquisition (e.g., change the illumination of a room), making it very difficult to measure how specific properties of the data affect performance. In this paper, we present AI Playground (AIP), an open-source, Unreal Engine-based tool for generating and labeling virtual image data. With AIP, it is trivial to capture the same image under different conditions (e.g., fidelity, lighting, etc.) and with different ground truths (e.g., depth or surface normal values). AIP is easily extendable and can be used with or without code. To validate our proposed tool, we generated eight datasets of otherwise identical but varying lighting and fidelity conditions. We then trained deep neural networks to predict (1) depth values, (2) surface normals, or (3) object labels and assessed each network's intra- and cross-dataset performance. Among other insights, we verified that sensitivity to different settings is problem-dependent. We confirmed the findings of other studies that segmentation models are very sensitive to fidelity, but we also found that they are just as sensitive to lighting. In contrast, depth and normal estimation models seem to be less sensitive to fidelity or lighting and more sensitive to the structure of the image. Finally, we tested our trained depth-estimation networks on two real-world datasets and obtained results comparable to training on real data alone, confirming that our virtual environments are realistic enough for real-world tasks.

  • 3 authors
·
Jul 12, 2020

Enhancing Whole Slide Pathology Foundation Models through Stain Normalization

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

  • 5 authors
·
Aug 1, 2024

LLM-driven Indoor Scene Layout Generation via Scaled Human-aligned Data Synthesis and Multi-Stage Preference Optimization

Automatic indoor layout generation has attracted increasing attention due to its potential in interior design, virtual environment construction, and embodied AI. Existing methods fall into two categories: prompt-driven approaches that leverage proprietary LLM services (e.g., GPT APIs) and learning-based methods trained on layout data upon diffusion-based models. Prompt-driven methods often suffer from spatial inconsistency and high computational costs, while learning-based methods are typically constrained by coarse relational graphs and limited datasets, restricting their generalization to diverse room categories. In this paper, we revisit LLM-based indoor layout generation and present 3D-SynthPlace, a large-scale dataset that combines synthetic layouts generated via a 'GPT synthesize, Human inspect' pipeline, upgraded from the 3D-Front dataset. 3D-SynthPlace contains nearly 17,000 scenes, covering four common room types -- bedroom, living room, kitchen, and bathroom -- enriched with diverse objects and high-level spatial annotations. We further introduce OptiScene, a strong open-source LLM optimized for indoor layout generation, fine-tuned based on our 3D-SynthPlace dataset through our two-stage training. For the warum-up stage I, we adopt supervised fine-tuning (SFT), which is taught to first generate high-level spatial descriptions then conditionally predict concrete object placements. For the reinforcing stage II, to better align the generated layouts with human design preferences, we apply multi-turn direct preference optimization (DPO), which significantly improving layout quality and generation success rates. Extensive experiments demonstrate that OptiScene outperforms traditional prompt-driven and learning-based baselines. Moreover, OptiScene shows promising potential in interactive tasks such as scene editing and robot navigation.

  • 8 authors
·
Jun 9

FaVoR: Features via Voxel Rendering for Camera Relocalization

Camera relocalization methods range from dense image alignment to direct camera pose regression from a query image. Among these, sparse feature matching stands out as an efficient, versatile, and generally lightweight approach with numerous applications. However, feature-based methods often struggle with significant viewpoint and appearance changes, leading to matching failures and inaccurate pose estimates. To overcome this limitation, we propose a novel approach that leverages a globally sparse yet locally dense 3D representation of 2D features. By tracking and triangulating landmarks over a sequence of frames, we construct a sparse voxel map optimized to render image patch descriptors observed during tracking. Given an initial pose estimate, we first synthesize descriptors from the voxels using volumetric rendering and then perform feature matching to estimate the camera pose. This methodology enables the generation of descriptors for unseen views, enhancing robustness to view changes. We extensively evaluate our method on the 7-Scenes and Cambridge Landmarks datasets. Our results show that our method significantly outperforms existing state-of-the-art feature representation techniques in indoor environments, achieving up to a 39% improvement in median translation error. Additionally, our approach yields comparable results to other methods for outdoor scenarios while maintaining lower memory and computational costs.

  • 4 authors
·
Sep 11, 2024

OpenFACADES: An Open Framework for Architectural Caption and Attribute Data Enrichment via Street View Imagery

Building properties, such as height, usage, and material composition, play a crucial role in spatial data infrastructures, supporting applications such as energy simulation, risk assessment, and environmental modeling. Despite their importance, comprehensive and high-quality building attribute data remain scarce in many urban areas. Recent advances have enabled the extraction and tagging of objective building attributes using remote sensing and street-level imagery. However, establishing a method and pipeline that integrates diverse open datasets, acquires holistic building imagery at scale, and infers comprehensive building attributes remains a significant challenge. Among the first, this study bridges the gaps by introducing OpenFACADES, an open framework that leverages multimodal crowdsourced data to enrich building profiles with both objective attributes and semantic descriptors through multimodal large language models. Our methodology proceeds in three major steps. First, we integrate street-level image metadata from Mapillary with OpenStreetMap geometries via isovist analysis, effectively identifying images that provide suitable vantage points for observing target buildings. Second, we automate the detection of building facades in panoramic imagery and tailor a reprojection approach to convert objects into holistic perspective views that approximate real-world observation. Third, we introduce an innovative approach that harnesses and systematically investigates the capabilities of open-source large vision-language models (VLMs) for multi-attribute prediction and open-vocabulary captioning in building-level analytics, leveraging a globally sourced dataset of 30,180 labeled images from seven cities. Evaluation shows that fine-tuned VLM excel in multi-attribute inference, outperforming single-attribute computer vision models and zero-shot ChatGPT-4o.

  • 5 authors
·
Apr 1

OpenM3D: Open Vocabulary Multi-view Indoor 3D Object Detection without Human Annotations

Open-vocabulary (OV) 3D object detection is an emerging field, yet its exploration through image-based methods remains limited compared to 3D point cloud-based methods. We introduce OpenM3D, a novel open-vocabulary multi-view indoor 3D object detector trained without human annotations. In particular, OpenM3D is a single-stage detector adapting the 2D-induced voxel features from the ImGeoNet model. To support OV, it is jointly trained with a class-agnostic 3D localization loss requiring high-quality 3D pseudo boxes and a voxel-semantic alignment loss requiring diverse pre-trained CLIP features. We follow the training setting of OV-3DET where posed RGB-D images are given but no human annotations of 3D boxes or classes are available. We propose a 3D Pseudo Box Generation method using a graph embedding technique that combines 2D segments into coherent 3D structures. Our pseudo-boxes achieve higher precision and recall than other methods, including the method proposed in OV-3DET. We further sample diverse CLIP features from 2D segments associated with each coherent 3D structure to align with the corresponding voxel feature. The key to training a highly accurate single-stage detector requires both losses to be learned toward high-quality targets. At inference, OpenM3D, a highly efficient detector, requires only multi-view images for input and demonstrates superior accuracy and speed (0.3 sec. per scene) on ScanNet200 and ARKitScenes indoor benchmarks compared to existing methods. We outperform a strong two-stage method that leverages our class-agnostic detector with a ViT CLIP-based OV classifier and a baseline incorporating multi-view depth estimator on both accuracy and speed.

  • 9 authors
·
Aug 27

SceneWeaver: All-in-One 3D Scene Synthesis with an Extensible and Self-Reflective Agent

Indoor scene synthesis has become increasingly important with the rise of Embodied AI, which requires 3D environments that are not only visually realistic but also physically plausible and functionally diverse. While recent approaches have advanced visual fidelity, they often remain constrained to fixed scene categories, lack sufficient object-level detail and physical consistency, and struggle to align with complex user instructions. In this work, we present SceneWeaver, a reflective agentic framework that unifies diverse scene synthesis paradigms through tool-based iterative refinement. At its core, SceneWeaver employs a language model-based planner to select from a suite of extensible scene generation tools, ranging from data-driven generative models to visual- and LLM-based methods, guided by self-evaluation of physical plausibility, visual realism, and semantic alignment with user input. This closed-loop reason-act-reflect design enables the agent to identify semantic inconsistencies, invoke targeted tools, and update the environment over successive iterations. Extensive experiments on both common and open-vocabulary room types demonstrate that SceneWeaver not only outperforms prior methods on physical, visual, and semantic metrics, but also generalizes effectively to complex scenes with diverse instructions, marking a step toward general-purpose 3D environment generation. Project website: https://scene-weaver.github.io/.

  • 4 authors
·
Sep 24 2

Habitat-Matterport 3D Dataset (HM3D): 1000 Large-scale 3D Environments for Embodied AI

We present the Habitat-Matterport 3D (HM3D) dataset. HM3D is a large-scale dataset of 1,000 building-scale 3D reconstructions from a diverse set of real-world locations. Each scene in the dataset consists of a textured 3D mesh reconstruction of interiors such as multi-floor residences, stores, and other private indoor spaces. HM3D surpasses existing datasets available for academic research in terms of physical scale, completeness of the reconstruction, and visual fidelity. HM3D contains 112.5k m^2 of navigable space, which is 1.4 - 3.7x larger than other building-scale datasets such as MP3D and Gibson. When compared to existing photorealistic 3D datasets such as Replica, MP3D, Gibson, and ScanNet, images rendered from HM3D have 20 - 85% higher visual fidelity w.r.t. counterpart images captured with real cameras, and HM3D meshes have 34 - 91% fewer artifacts due to incomplete surface reconstruction. The increased scale, fidelity, and diversity of HM3D directly impacts the performance of embodied AI agents trained using it. In fact, we find that HM3D is `pareto optimal' in the following sense -- agents trained to perform PointGoal navigation on HM3D achieve the highest performance regardless of whether they are evaluated on HM3D, Gibson, or MP3D. No similar claim can be made about training on other datasets. HM3D-trained PointNav agents achieve 100% performance on Gibson-test dataset, suggesting that it might be time to retire that episode dataset.

  • 13 authors
·
Sep 16, 2021 1

DebSDF: Delving into the Details and Bias of Neural Indoor Scene Reconstruction

In recent years, the neural implicit surface has emerged as a powerful representation for multi-view surface reconstruction due to its simplicity and state-of-the-art performance. However, reconstructing smooth and detailed surfaces in indoor scenes from multi-view images presents unique challenges. Indoor scenes typically contain large texture-less regions, making the photometric loss unreliable for optimizing the implicit surface. Previous work utilizes monocular geometry priors to improve the reconstruction in indoor scenes. However, monocular priors often contain substantial errors in thin structure regions due to domain gaps and the inherent inconsistencies when derived independently from different views. This paper presents DebSDF to address these challenges, focusing on the utilization of uncertainty in monocular priors and the bias in SDF-based volume rendering. We propose an uncertainty modeling technique that associates larger uncertainties with larger errors in the monocular priors. High-uncertainty priors are then excluded from optimization to prevent bias. This uncertainty measure also informs an importance-guided ray sampling and adaptive smoothness regularization, enhancing the learning of fine structures. We further introduce a bias-aware signed distance function to density transformation that takes into account the curvature and the angle between the view direction and the SDF normals to reconstruct fine details better. Our approach has been validated through extensive experiments on several challenging datasets, demonstrating improved qualitative and quantitative results in reconstructing thin structures in indoor scenes, thereby outperforming previous work.

  • 4 authors
·
Aug 29, 2023

See through the Dark: Learning Illumination-affined Representations for Nighttime Occupancy Prediction

Occupancy prediction aims to estimate the 3D spatial distribution of occupied regions along with their corresponding semantic labels. Existing vision-based methods perform well on daytime benchmarks but struggle in nighttime scenarios due to limited visibility and challenging lighting conditions. To address these challenges, we propose LIAR, a novel framework that learns illumination-affined representations. LIAR first introduces Selective Low-light Image Enhancement (SLLIE), which leverages the illumination priors from daytime scenes to adaptively determine whether a nighttime image is genuinely dark or sufficiently well-lit, enabling more targeted global enhancement. Building on the illumination maps generated by SLLIE, LIAR further incorporates two illumination-aware components: 2D Illumination-guided Sampling (2D-IGS) and 3D Illumination-driven Projection (3D-IDP), to respectively tackle local underexposure and overexposure. Specifically, 2D-IGS modulates feature sampling positions according to illumination maps, assigning larger offsets to darker regions and smaller ones to brighter regions, thereby alleviating feature degradation in underexposed areas. Subsequently, 3D-IDP enhances semantic understanding in overexposed regions by constructing illumination intensity fields and supplying refined residual queries to the BEV context refinement process. Extensive experiments on both real and synthetic datasets demonstrate the superior performance of LIAR under challenging nighttime scenarios. The source code and pretrained models are available https://github.com/yanzq95/LIAR{here}.

  • 5 authors
·
May 26

Open-Universe Indoor Scene Generation using LLM Program Synthesis and Uncurated Object Databases

We present a system for generating indoor scenes in response to text prompts. The prompts are not limited to a fixed vocabulary of scene descriptions, and the objects in generated scenes are not restricted to a fixed set of object categories -- we call this setting indoor scene generation. Unlike most prior work on indoor scene generation, our system does not require a large training dataset of existing 3D scenes. Instead, it leverages the world knowledge encoded in pre-trained large language models (LLMs) to synthesize programs in a domain-specific layout language that describe objects and spatial relations between them. Executing such a program produces a specification of a constraint satisfaction problem, which the system solves using a gradient-based optimization scheme to produce object positions and orientations. To produce object geometry, the system retrieves 3D meshes from a database. Unlike prior work which uses databases of category-annotated, mutually-aligned meshes, we develop a pipeline using vision-language models (VLMs) to retrieve meshes from massive databases of un-annotated, inconsistently-aligned meshes. Experimental evaluations show that our system outperforms generative models trained on 3D data for traditional, closed-universe scene generation tasks; it also outperforms a recent LLM-based layout generation method on open-universe scene generation.

  • 10 authors
·
Feb 4, 2024

ZoeDepth: Zero-shot Transfer by Combining Relative and Metric Depth

This paper tackles the problem of depth estimation from a single image. Existing work either focuses on generalization performance disregarding metric scale, i.e. relative depth estimation, or state-of-the-art results on specific datasets, i.e. metric depth estimation. We propose the first approach that combines both worlds, leading to a model with excellent generalization performance while maintaining metric scale. Our flagship model, ZoeD-M12-NK, is pre-trained on 12 datasets using relative depth and fine-tuned on two datasets using metric depth. We use a lightweight head with a novel bin adjustment design called metric bins module for each domain. During inference, each input image is automatically routed to the appropriate head using a latent classifier. Our framework admits multiple configurations depending on the datasets used for relative depth pre-training and metric fine-tuning. Without pre-training, we can already significantly improve the state of the art (SOTA) on the NYU Depth v2 indoor dataset. Pre-training on twelve datasets and fine-tuning on the NYU Depth v2 indoor dataset, we can further improve SOTA for a total of 21% in terms of relative absolute error (REL). Finally, ZoeD-M12-NK is the first model that can jointly train on multiple datasets (NYU Depth v2 and KITTI) without a significant drop in performance and achieve unprecedented zero-shot generalization performance to eight unseen datasets from both indoor and outdoor domains. The code and pre-trained models are publicly available at https://github.com/isl-org/ZoeDepth .

  • 5 authors
·
Feb 23, 2023

A Multimodal Knowledge-enhanced Whole-slide Pathology Foundation Model

Remarkable strides in computational pathology have been made in the task-agnostic foundation model that advances the performance of a wide array of downstream clinical tasks. Despite the promising performance, there are still several challenges. First, prior works have resorted to either vision-only or image-caption data, disregarding pathology reports with more clinically authentic information from pathologists and gene expression profiles which respectively offer distinct knowledge for versatile clinical applications. Second, the current progress in pathology FMs predominantly concentrates on the patch level, where the restricted context of patch-level pretraining fails to capture whole-slide patterns. Even recent slide-level FMs still struggle to provide whole-slide context for patch representation. In this study, for the first time, we develop a pathology foundation model incorporating three levels of modalities: pathology slides, pathology reports, and gene expression data, which resulted in 26,169 slide-level modality pairs from 10,275 patients across 32 cancer types, amounting to over 116 million pathological patch images. To leverage these data for CPath, we propose a novel whole-slide pretraining paradigm that injects the multimodal whole-slide context into the patch representation, called Multimodal Self-TAught PRetraining (mSTAR). The proposed paradigm revolutionizes the pretraining workflow for CPath, enabling the pathology FM to acquire the whole-slide context. To the best of our knowledge, this is the first attempt to incorporate three modalities at the whole-slide context for enhancing pathology FMs. To systematically evaluate the capabilities of mSTAR, we built the largest spectrum of oncological benchmark, spanning 7 categories of oncological applications in 15 types of 97 practical oncological tasks.

  • 19 authors
·
Jul 22, 2024

FreeReg: Image-to-Point Cloud Registration Leveraging Pretrained Diffusion Models and Monocular Depth Estimators

Matching cross-modality features between images and point clouds is a fundamental problem for image-to-point cloud registration. However, due to the modality difference between images and points, it is difficult to learn robust and discriminative cross-modality features by existing metric learning methods for feature matching. Instead of applying metric learning on cross-modality data, we propose to unify the modality between images and point clouds by pretrained large-scale models first, and then establish robust correspondence within the same modality. We show that the intermediate features, called diffusion features, extracted by depth-to-image diffusion models are semantically consistent between images and point clouds, which enables the building of coarse but robust cross-modality correspondences. We further extract geometric features on depth maps produced by the monocular depth estimator. By matching such geometric features, we significantly improve the accuracy of the coarse correspondences produced by diffusion features. Extensive experiments demonstrate that without any task-specific training, direct utilization of both features produces accurate image-to-point cloud registration. On three public indoor and outdoor benchmarks, the proposed method averagely achieves a 20.6 percent improvement in Inlier Ratio, a three-fold higher Inlier Number, and a 48.6 percent improvement in Registration Recall than existing state-of-the-arts.

  • 7 authors
·
Oct 5, 2023

M3DLayout: A Multi-Source Dataset of 3D Indoor Layouts and Structured Descriptions for 3D Generation

In text-driven 3D scene generation, object layout serves as a crucial intermediate representation that bridges high-level language instructions with detailed geometric output. It not only provides a structural blueprint for ensuring physical plausibility but also supports semantic controllability and interactive editing. However, the learning capabilities of current 3D indoor layout generation models are constrained by the limited scale, diversity, and annotation quality of existing datasets. To address this, we introduce M3DLayout, a large-scale, multi-source dataset for 3D indoor layout generation. M3DLayout comprises 15,080 layouts and over 258k object instances, integrating three distinct sources: real-world scans, professional CAD designs, and procedurally generated scenes. Each layout is paired with detailed structured text describing global scene summaries, relational placements of large furniture, and fine-grained arrangements of smaller items. This diverse and richly annotated resource enables models to learn complex spatial and semantic patterns across a wide variety of indoor environments. To assess the potential of M3DLayout, we establish a benchmark using a text-conditioned diffusion model. Experimental results demonstrate that our dataset provides a solid foundation for training layout generation models. Its multi-source composition enhances diversity, notably through the Inf3DLayout subset which provides rich small-object information, enabling the generation of more complex and detailed scenes. We hope that M3DLayout can serve as a valuable resource for advancing research in text-driven 3D scene synthesis.

  • 7 authors
·
Sep 28

On the Importance of Text Preprocessing for Multimodal Representation Learning and Pathology Report Generation

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.

  • 6 authors
·
Feb 26

Patherea: Cell Detection and Classification for the 2020s

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

  • 6 authors
·
Dec 20, 2024

UAV-assisted Visual SLAM Generating Reconstructed 3D Scene Graphs in GPS-denied Environments

Aerial robots play a vital role in various applications where the situational awareness of the robots concerning the environment is a fundamental demand. As one such use case, drones in GPS-denied environments require equipping with different sensors (e.g., vision sensors) that provide reliable sensing results while performing pose estimation and localization. In this paper, reconstructing the maps of indoor environments alongside generating 3D scene graphs for a high-level representation using a camera mounted on a drone is targeted. Accordingly, an aerial robot equipped with a companion computer and an RGB-D camera was built and employed to be appropriately integrated with a Visual Simultaneous Localization and Mapping (VSLAM) framework proposed by the authors. To enhance the situational awareness of the robot while reconstructing maps, various structural elements, including doors and walls, were labeled with printed fiducial markers, and a dictionary of the topological relations among them was fed to the system. The VSLAM system detects markers and reconstructs the map of the indoor areas enriched with higher-level semantic entities, including corridors and rooms. Another achievement is generating multi-layered vision-based situational graphs containing enhanced hierarchical representations of the indoor environment. In this regard, integrating VSLAM into the employed drone is the primary target of this paper to provide an end-to-end robot application for GPS-denied environments. To show the practicality of the system, various real-world condition experiments have been conducted in indoor scenarios with dissimilar structural layouts. Evaluations show the proposed drone application can perform adequately w.r.t. the ground-truth data and its baseline.

  • 5 authors
·
Feb 12, 2024

EmbodiedOcc++: Boosting Embodied 3D Occupancy Prediction with Plane Regularization and Uncertainty Sampler

Online 3D occupancy prediction provides a comprehensive spatial understanding of embodied environments. While the innovative EmbodiedOcc framework utilizes 3D semantic Gaussians for progressive indoor occupancy prediction, it overlooks the geometric characteristics of indoor environments, which are primarily characterized by planar structures. This paper introduces EmbodiedOcc++, enhancing the original framework with two key innovations: a Geometry-guided Refinement Module (GRM) that constrains Gaussian updates through plane regularization, along with a Semantic-aware Uncertainty Sampler (SUS) that enables more effective updates in overlapping regions between consecutive frames. GRM regularizes the position update to align with surface normals. It determines the adaptive regularization weight using curvature-based and depth-based constraints, allowing semantic Gaussians to align accurately with planar surfaces while adapting in complex regions. To effectively improve geometric consistency from different views, SUS adaptively selects proper Gaussians to update. Comprehensive experiments on the EmbodiedOcc-ScanNet benchmark demonstrate that EmbodiedOcc++ achieves state-of-the-art performance across different settings. Our method demonstrates improved edge accuracy and retains more geometric details while ensuring computational efficiency, which is essential for online embodied perception. The code will be released at: https://github.com/PKUHaoWang/EmbodiedOcc2.

  • 9 authors
·
Apr 13

ScaleDepth: Decomposing Metric Depth Estimation into Scale Prediction and Relative Depth Estimation

Estimating depth from a single image is a challenging visual task. Compared to relative depth estimation, metric depth estimation attracts more attention due to its practical physical significance and critical applications in real-life scenarios. However, existing metric depth estimation methods are typically trained on specific datasets with similar scenes, facing challenges in generalizing across scenes with significant scale variations. To address this challenge, we propose a novel monocular depth estimation method called ScaleDepth. Our method decomposes metric depth into scene scale and relative depth, and predicts them through a semantic-aware scale prediction (SASP) module and an adaptive relative depth estimation (ARDE) module, respectively. The proposed ScaleDepth enjoys several merits. First, the SASP module can implicitly combine structural and semantic features of the images to predict precise scene scales. Second, the ARDE module can adaptively estimate the relative depth distribution of each image within a normalized depth space. Third, our method achieves metric depth estimation for both indoor and outdoor scenes in a unified framework, without the need for setting the depth range or fine-tuning model. Extensive experiments demonstrate that our method attains state-of-the-art performance across indoor, outdoor, unconstrained, and unseen scenes. Project page: https://ruijiezhu94.github.io/ScaleDepth

  • 6 authors
·
Jul 11, 2024 1

Zero-Shot Dual-Path Integration Framework for Open-Vocabulary 3D Instance Segmentation

Open-vocabulary 3D instance segmentation transcends traditional closed-vocabulary methods by enabling the identification of both previously seen and unseen objects in real-world scenarios. It leverages a dual-modality approach, utilizing both 3D point clouds and 2D multi-view images to generate class-agnostic object mask proposals. Previous efforts predominantly focused on enhancing 3D mask proposal models; consequently, the information that could come from 2D association to 3D was not fully exploited. This bias towards 3D data, while effective for familiar indoor objects, limits the system's adaptability to new and varied object types, where 2D models offer greater utility. Addressing this gap, we introduce Zero-Shot Dual-Path Integration Framework that equally values the contributions of both 3D and 2D modalities. Our framework comprises three components: 3D pathway, 2D pathway, and Dual-Path Integration. 3D pathway generates spatially accurate class-agnostic mask proposals of common indoor objects from 3D point cloud data using a pre-trained 3D model, while 2D pathway utilizes pre-trained open-vocabulary instance segmentation model to identify a diverse array of object proposals from multi-view RGB-D images. In Dual-Path Integration, our Conditional Integration process, which operates in two stages, filters and merges the proposals from both pathways adaptively. This process harmonizes output proposals to enhance segmentation capabilities. Our framework, utilizing pre-trained models in a zero-shot manner, is model-agnostic and demonstrates superior performance on both seen and unseen data, as evidenced by comprehensive evaluations on the ScanNet200 and qualitative results on ARKitScenes datasets.

  • 6 authors
·
Aug 16, 2024

LPA3D: 3D Room-Level Scene Generation from In-the-Wild Images

Generating realistic, room-level indoor scenes with semantically plausible and detailed appearances from in-the-wild images is crucial for various applications in VR, AR, and robotics. The success of NeRF-based generative methods indicates a promising direction to address this challenge. However, unlike their success at the object level, existing scene-level generative methods require additional information, such as multiple views, depth images, or semantic guidance, rather than relying solely on RGB images. This is because NeRF-based methods necessitate prior knowledge of camera poses, which is challenging to approximate for indoor scenes due to the complexity of defining alignment and the difficulty of globally estimating poses from a single image, given the unseen parts behind the camera. To address this challenge, we redefine global poses within the framework of Local-Pose-Alignment (LPA) -- an anchor-based multi-local-coordinate system that uses a selected number of anchors as the roots of these coordinates. Building on this foundation, we introduce LPA-GAN, a novel NeRF-based generative approach that incorporates specific modifications to estimate the priors of camera poses under LPA. It also co-optimizes the pose predictor and scene generation processes. Our ablation study and comparisons with straightforward extensions of NeRF-based object generative methods demonstrate the effectiveness of our approach. Furthermore, visual comparisons with other techniques reveal that our method achieves superior view-to-view consistency and semantic normality.

  • 5 authors
·
Apr 3

The Audio-Visual BatVision Dataset for Research on Sight and Sound

Vision research showed remarkable success in understanding our world, propelled by datasets of images and videos. Sensor data from radar, LiDAR and cameras supports research in robotics and autonomous driving for at least a decade. However, while visual sensors may fail in some conditions, sound has recently shown potential to complement sensor data. Simulated room impulse responses (RIR) in 3D apartment-models became a benchmark dataset for the community, fostering a range of audiovisual research. In simulation, depth is predictable from sound, by learning bat-like perception with a neural network. Concurrently, the same was achieved in reality by using RGB-D images and echoes of chirping sounds. Biomimicking bat perception is an exciting new direction but needs dedicated datasets to explore the potential. Therefore, we collected the BatVision dataset to provide large-scale echoes in complex real-world scenes to the community. We equipped a robot with a speaker to emit chirps and a binaural microphone to record their echoes. Synchronized RGB-D images from the same perspective provide visual labels of traversed spaces. We sampled modern US office spaces to historic French university grounds, indoor and outdoor with large architectural variety. This dataset will allow research on robot echolocation, general audio-visual tasks and sound ph{\ae}nomena unavailable in simulated data. We show promising results for audio-only depth prediction and show how state-of-the-art work developed for simulated data can also succeed on our dataset. Project page: https://amandinebtto.github.io/Batvision-Dataset/

  • 4 authors
·
Mar 13, 2023

Integrating Biological Knowledge for Robust Microscopy Image Profiling on De Novo Cell Lines

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

  • 4 authors
·
Jul 14

PixCell: A generative foundation model for digital histopathology images

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

  • 13 authors
·
Jun 5

MIPHEI-ViT: Multiplex Immunofluorescence Prediction from H&E Images using ViT Foundation Models

Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tissue architecture. On the other hand, multiplex immunofluorescence (mIF) enables more precise cell type identification via proteomic markers, but has yet to achieve widespread clinical adoption due to cost and logistical constraints. To bridge this gap, we introduce MIPHEI (Multiplex Immunofluorescence Prediction from H&E), a U-Net-inspired architecture that integrates state-of-the-art ViT foundation models as encoders to predict mIF signals from H&E images. MIPHEI targets a comprehensive panel of markers spanning nuclear content, immune lineages (T cells, B cells, myeloid), epithelium, stroma, vasculature, and proliferation. We train our model using the publicly available ORION dataset of restained H&E and mIF images from colorectal cancer tissue, and validate it on two independent datasets. MIPHEI achieves accurate cell-type classification from H&E alone, with F1 scores of 0.88 for Pan-CK, 0.57 for CD3e, 0.56 for SMA, 0.36 for CD68, and 0.30 for CD20, substantially outperforming both a state-of-the-art baseline and a random classifier for most markers. Our results indicate that our model effectively captures the complex relationships between nuclear morphologies in their tissue context, as visible in H&E images and molecular markers defining specific cell types. MIPHEI offers a promising step toward enabling cell-type-aware analysis of large-scale H&E datasets, in view of uncovering relationships between spatial cellular organization and patient outcomes.

  • 5 authors
·
May 15

Global-Local Tree Search for Language Guided 3D Scene Generation

Large Vision-Language Models (VLMs), such as GPT-4, have achieved remarkable success across various fields. However, there are few studies on 3D indoor scene generation with VLMs. This paper considers this task as a planning problem subject to spatial and layout common sense constraints. To solve the problem with a VLM, we propose a new global-local tree search algorithm. Globally, the method places each object sequentially and explores multiple placements during each placement process, where the problem space is represented as a tree. To reduce the depth of the tree, we decompose the scene structure hierarchically, i.e. room level, region level, floor object level, and supported object level. The algorithm independently generates the floor objects in different regions and supported objects placed on different floor objects. Locally, we also decompose the sub-task, the placement of each object, into multiple steps. The algorithm searches the tree of problem space. To leverage the VLM model to produce positions of objects, we discretize the top-down view space as a dense grid and fill each cell with diverse emojis to make to cells distinct. We prompt the VLM with the emoji grid and the VLM produces a reasonable location for the object by describing the position with the name of emojis. The quantitative and qualitative experimental results illustrate our approach generates more plausible 3D scenes than state-of-the-art approaches. Our source code is available at https://github.com/dw-dengwei/TreeSearchGen .

  • 3 authors
·
Mar 24 2

Hierarchically-Structured Open-Vocabulary Indoor Scene Synthesis with Pre-trained Large Language Model

Indoor scene synthesis aims to automatically produce plausible, realistic and diverse 3D indoor scenes, especially given arbitrary user requirements. Recently, the promising generalization ability of pre-trained large language models (LLM) assist in open-vocabulary indoor scene synthesis. However, the challenge lies in converting the LLM-generated outputs into reasonable and physically feasible scene layouts. In this paper, we propose to generate hierarchically structured scene descriptions with LLM and then compute the scene layouts. Specifically, we train a hierarchy-aware network to infer the fine-grained relative positions between objects and design a divide-and-conquer optimization to solve for scene layouts. The advantages of using hierarchically structured scene representation are two-fold. First, the hierarchical structure provides a rough grounding for object arrangement, which alleviates contradictory placements with dense relations and enhances the generalization ability of the network to infer fine-grained placements. Second, it naturally supports the divide-and-conquer optimization, by first arranging the sub-scenes and then the entire scene, to more effectively solve for a feasible layout. We conduct extensive comparison experiments and ablation studies with both qualitative and quantitative evaluations to validate the effectiveness of our key designs with the hierarchically structured scene representation. Our approach can generate more reasonable scene layouts while better aligned with the user requirements and LLM descriptions. We also present open-vocabulary scene synthesis and interactive scene design results to show the strength of our approach in the applications.

  • 6 authors
·
Feb 15

Ctrl-Room: Controllable Text-to-3D Room Meshes Generation with Layout Constraints

Text-driven 3D indoor scene generation could be useful for gaming, film industry, and AR/VR applications. However, existing methods cannot faithfully capture the room layout, nor do they allow flexible editing of individual objects in the room. To address these problems, we present Ctrl-Room, which is able to generate convincing 3D rooms with designer-style layouts and high-fidelity textures from just a text prompt. Moreover, Ctrl-Room enables versatile interactive editing operations such as resizing or moving individual furniture items. Our key insight is to separate the modeling of layouts and appearance. %how to model the room that takes into account both scene texture and geometry at the same time. To this end, Our proposed method consists of two stages, a `Layout Generation Stage' and an `Appearance Generation Stage'. The `Layout Generation Stage' trains a text-conditional diffusion model to learn the layout distribution with our holistic scene code parameterization. Next, the `Appearance Generation Stage' employs a fine-tuned ControlNet to produce a vivid panoramic image of the room guided by the 3D scene layout and text prompt. In this way, we achieve a high-quality 3D room with convincing layouts and lively textures. Benefiting from the scene code parameterization, we can easily edit the generated room model through our mask-guided editing module, without expensive editing-specific training. Extensive experiments on the Structured3D dataset demonstrate that our method outperforms existing methods in producing more reasonable, view-consistent, and editable 3D rooms from natural language prompts.

  • 4 authors
·
Oct 5, 2023

EverLight: Indoor-Outdoor Editable HDR Lighting Estimation

Because of the diversity in lighting environments, existing illumination estimation techniques have been designed explicitly on indoor or outdoor environments. Methods have focused specifically on capturing accurate energy (e.g., through parametric lighting models), which emphasizes shading and strong cast shadows; or producing plausible texture (e.g., with GANs), which prioritizes plausible reflections. Approaches which provide editable lighting capabilities have been proposed, but these tend to be with simplified lighting models, offering limited realism. In this work, we propose to bridge the gap between these recent trends in the literature, and propose a method which combines a parametric light model with 360{\deg} panoramas, ready to use as HDRI in rendering engines. We leverage recent advances in GAN-based LDR panorama extrapolation from a regular image, which we extend to HDR using parametric spherical gaussians. To achieve this, we introduce a novel lighting co-modulation method that injects lighting-related features throughout the generator, tightly coupling the original or edited scene illumination within the panorama generation process. In our representation, users can easily edit light direction, intensity, number, etc. to impact shading while providing rich, complex reflections while seamlessly blending with the edits. Furthermore, our method encompasses indoor and outdoor environments, demonstrating state-of-the-art results even when compared to domain-specific methods.

  • 4 authors
·
Apr 25, 2023

ParaHome: Parameterizing Everyday Home Activities Towards 3D Generative Modeling of Human-Object Interactions

To enable machines to learn how humans interact with the physical world in our daily activities, it is crucial to provide rich data that encompasses the 3D motion of humans as well as the motion of objects in a learnable 3D representation. Ideally, this data should be collected in a natural setup, capturing the authentic dynamic 3D signals during human-object interactions. To address this challenge, we introduce the ParaHome system, designed to capture and parameterize dynamic 3D movements of humans and objects within a common home environment. Our system consists of a multi-view setup with 70 synchronized RGB cameras, as well as wearable motion capture devices equipped with an IMU-based body suit and hand motion capture gloves. By leveraging the ParaHome system, we collect a novel large-scale dataset of human-object interaction. Notably, our dataset offers key advancement over existing datasets in three main aspects: (1) capturing 3D body and dexterous hand manipulation motion alongside 3D object movement within a contextual home environment during natural activities; (2) encompassing human interaction with multiple objects in various episodic scenarios with corresponding descriptions in texts; (3) including articulated objects with multiple parts expressed with parameterized articulations. Building upon our dataset, we introduce new research tasks aimed at building a generative model for learning and synthesizing human-object interactions in a real-world room setting.

  • 4 authors
·
Jan 18, 2024

ShAPO: Implicit Representations for Multi-Object Shape, Appearance, and Pose Optimization

Our method studies the complex task of object-centric 3D understanding from a single RGB-D observation. As it is an ill-posed problem, existing methods suffer from low performance for both 3D shape and 6D pose and size estimation in complex multi-object scenarios with occlusions. We present ShAPO, a method for joint multi-object detection, 3D textured reconstruction, 6D object pose and size estimation. Key to ShAPO is a single-shot pipeline to regress shape, appearance and pose latent codes along with the masks of each object instance, which is then further refined in a sparse-to-dense fashion. A novel disentangled shape and appearance database of priors is first learned to embed objects in their respective shape and appearance space. We also propose a novel, octree-based differentiable optimization step, allowing us to further improve object shape, pose and appearance simultaneously under the learned latent space, in an analysis-by-synthesis fashion. Our novel joint implicit textured object representation allows us to accurately identify and reconstruct novel unseen objects without having access to their 3D meshes. Through extensive experiments, we show that our method, trained on simulated indoor scenes, accurately regresses the shape, appearance and pose of novel objects in the real-world with minimal fine-tuning. Our method significantly out-performs all baselines on the NOCS dataset with an 8% absolute improvement in mAP for 6D pose estimation. Project page: https://zubair-irshad.github.io/projects/ShAPO.html

  • 6 authors
·
Jul 27, 2022

PLUTO: Pathology-Universal Transformer

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

  • 33 authors
·
May 13, 2024

EndoPBR: Material and Lighting Estimation for Photorealistic Surgical Simulations via Physically-based Rendering

The lack of labeled datasets in 3D vision for surgical scenes inhibits the development of robust 3D reconstruction algorithms in the medical domain. Despite the popularity of Neural Radiance Fields and 3D Gaussian Splatting in the general computer vision community, these systems have yet to find consistent success in surgical scenes due to challenges such as non-stationary lighting and non-Lambertian surfaces. As a result, the need for labeled surgical datasets continues to grow. In this work, we introduce a differentiable rendering framework for material and lighting estimation from endoscopic images and known geometry. Compared to previous approaches that model lighting and material jointly as radiance, we explicitly disentangle these scene properties for robust and photorealistic novel view synthesis. To disambiguate the training process, we formulate domain-specific properties inherent in surgical scenes. Specifically, we model the scene lighting as a simple spotlight and material properties as a bidirectional reflectance distribution function, parameterized by a neural network. By grounding color predictions in the rendering equation, we can generate photorealistic images at arbitrary camera poses. We evaluate our method with various sequences from the Colonoscopy 3D Video Dataset and show that our method produces competitive novel view synthesis results compared with other approaches. Furthermore, we demonstrate that synthetic data can be used to develop 3D vision algorithms by finetuning a depth estimation model with our rendered outputs. Overall, we see that the depth estimation performance is on par with fine-tuning with the original real images.

  • 2 authors
·
Feb 27

SceneSplat: Gaussian Splatting-based Scene Understanding with Vision-Language Pretraining

Recognizing arbitrary or previously unseen categories is essential for comprehensive real-world 3D scene understanding. Currently, all existing methods rely on 2D or textual modalities during training, or together at inference. This highlights a clear absence of a model capable of processing 3D data alone for learning semantics end-to-end, along with the necessary data to train such a model. Meanwhile, 3D Gaussian Splatting (3DGS) has emerged as the de facto standard for 3D scene representation across various vision tasks. However, effectively integrating semantic reasoning into 3DGS in a generalizable fashion remains an open challenge. To address these limitations we introduce SceneSplat, to our knowledge the first large-scale 3D indoor scene understanding approach that operates natively on 3DGS. Furthermore, we propose a self-supervised learning scheme that unlocks rich 3D feature learning from unlabeled scenes. In order to power the proposed methods, we introduce SceneSplat-7K, the first large-scale 3DGS dataset for indoor scenes, comprising of 6868 scenes derived from 7 established datasets like ScanNet, Matterport3D, etc. Generating SceneSplat-7K required computational resources equivalent to 119 GPU-days on an L4 GPU, enabling standardized benchmarking for 3DGS-based reasoning for indoor scenes. Our exhaustive experiments on SceneSplat-7K demonstrate the significant benefit of the proposed methods over the established baselines.

  • 13 authors
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Mar 23

LighthouseGS: Indoor Structure-aware 3D Gaussian Splatting for Panorama-Style Mobile Captures

Recent advances in 3D Gaussian Splatting (3DGS) have enabled real-time novel view synthesis (NVS) with impressive quality in indoor scenes. However, achieving high-fidelity rendering requires meticulously captured images covering the entire scene, limiting accessibility for general users. We aim to develop a practical 3DGS-based NVS framework using simple panorama-style motion with a handheld camera (e.g., mobile device). While convenient, this rotation-dominant motion and narrow baseline make accurate camera pose and 3D point estimation challenging, especially in textureless indoor scenes. To address these challenges, we propose LighthouseGS, a novel framework inspired by the lighthouse-like sweeping motion of panoramic views. LighthouseGS leverages rough geometric priors, such as mobile device camera poses and monocular depth estimation, and utilizes the planar structures often found in indoor environments. We present a new initialization method called plane scaffold assembly to generate consistent 3D points on these structures, followed by a stable pruning strategy to enhance geometry and optimization stability. Additionally, we introduce geometric and photometric corrections to resolve inconsistencies from motion drift and auto-exposure in mobile devices. Tested on collected real and synthetic indoor scenes, LighthouseGS delivers photorealistic rendering, surpassing state-of-the-art methods and demonstrating the potential for panoramic view synthesis and object placement.

  • 7 authors
·
Jul 8

Unposed Sparse Views Room Layout Reconstruction in the Age of Pretrain Model

Room layout estimation from multiple-perspective images is poorly investigated due to the complexities that emerge from multi-view geometry, which requires muti-step solutions such as camera intrinsic and extrinsic estimation, image matching, and triangulation. However, in 3D reconstruction, the advancement of recent 3D foundation models such as DUSt3R has shifted the paradigm from the traditional multi-step structure-from-motion process to an end-to-end single-step approach. To this end, we introduce Plane-DUSt3R, a novel method for multi-view room layout estimation leveraging the 3D foundation model DUSt3R. Plane-DUSt3R incorporates the DUSt3R framework and fine-tunes on a room layout dataset (Structure3D) with a modified objective to estimate structural planes. By generating uniform and parsimonious results, Plane-DUSt3R enables room layout estimation with only a single post-processing step and 2D detection results. Unlike previous methods that rely on single-perspective or panorama image, Plane-DUSt3R extends the setting to handle multiple-perspective images. Moreover, it offers a streamlined, end-to-end solution that simplifies the process and reduces error accumulation. Experimental results demonstrate that Plane-DUSt3R not only outperforms state-of-the-art methods on the synthetic dataset but also proves robust and effective on in the wild data with different image styles such as cartoon.Our code is available at: https://github.com/justacar/Plane-DUSt3R

  • 6 authors
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Feb 23 3

Behind the Veil: Enhanced Indoor 3D Scene Reconstruction with Occluded Surfaces Completion

In this paper, we present a novel indoor 3D reconstruction method with occluded surface completion, given a sequence of depth readings. Prior state-of-the-art (SOTA) methods only focus on the reconstruction of the visible areas in a scene, neglecting the invisible areas due to the occlusions, e.g., the contact surface between furniture, occluded wall and floor. Our method tackles the task of completing the occluded scene surfaces, resulting in a complete 3D scene mesh. The core idea of our method is learning 3D geometry prior from various complete scenes to infer the occluded geometry of an unseen scene from solely depth measurements. We design a coarse-fine hierarchical octree representation coupled with a dual-decoder architecture, i.e., Geo-decoder and 3D Inpainter, which jointly reconstructs the complete 3D scene geometry. The Geo-decoder with detailed representation at fine levels is optimized online for each scene to reconstruct visible surfaces. The 3D Inpainter with abstract representation at coarse levels is trained offline using various scenes to complete occluded surfaces. As a result, while the Geo-decoder is specialized for an individual scene, the 3D Inpainter can be generally applied across different scenes. We evaluate the proposed method on the 3D Completed Room Scene (3D-CRS) and iTHOR datasets, significantly outperforming the SOTA methods by a gain of 16.8% and 24.2% in terms of the completeness of 3D reconstruction. 3D-CRS dataset including a complete 3D mesh of each scene is provided at project webpage.

  • 7 authors
·
Apr 3, 2024

SmartHome-Bench: A Comprehensive Benchmark for Video Anomaly Detection in Smart Homes Using Multi-Modal Large Language Models

Video anomaly detection (VAD) is essential for enhancing safety and security by identifying unusual events across different environments. Existing VAD benchmarks, however, are primarily designed for general-purpose scenarios, neglecting the specific characteristics of smart home applications. To bridge this gap, we introduce SmartHome-Bench, the first comprehensive benchmark specially designed for evaluating VAD in smart home scenarios, focusing on the capabilities of multi-modal large language models (MLLMs). Our newly proposed benchmark consists of 1,203 videos recorded by smart home cameras, organized according to a novel anomaly taxonomy that includes seven categories, such as Wildlife, Senior Care, and Baby Monitoring. Each video is meticulously annotated with anomaly tags, detailed descriptions, and reasoning. We further investigate adaptation methods for MLLMs in VAD, assessing state-of-the-art closed-source and open-source models with various prompting techniques. Results reveal significant limitations in the current models' ability to detect video anomalies accurately. To address these limitations, we introduce the Taxonomy-Driven Reflective LLM Chain (TRLC), a new LLM chaining framework that achieves a notable 11.62% improvement in detection accuracy. The benchmark dataset and code are publicly available at https://github.com/Xinyi-0724/SmartHome-Bench-LLM.

  • 7 authors
·
Jun 15

ChAda-ViT : Channel Adaptive Attention for Joint Representation Learning of Heterogeneous Microscopy Images

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDRCell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and channel counts varying from 1 to 10 per experiment. Our proposed architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. Code and Data to be released soon.

  • 7 authors
·
Nov 26, 2023

Flying Triangulation - towards the 3D movie camera

Flying Triangulation sensors enable a free-hand and motion-robust 3D data acquisition of complex shaped objects. The measurement principle is based on a multi-line light-sectioning approach and uses sophisticated algorithms for real-time registration (S. Ettl et al., Appl. Opt. 51 (2012) 281-289). As "single-shot principle", light sectioning enables the option to get surface data from one single camera exposure. But there is a drawback: A pixel-dense measurement is not possible because of fundamental information-theoretical reasons. By "pixel-dense" we understand that each pixel displays individually measured distance information, neither interpolated from its neighbour pixels nor using lateral context information. Hence, for monomodal single-shot principles, the 3D data generated from one 2D raw image display a significantly lower space-bandwidth than the camera permits. This is the price one must pay for motion robustness. Currently, our sensors project about 10 lines (each with 1000 pixels), reaching an considerable lower data efficiency than theoretically possible for a single-shot sensor. Our aim is to push Flying Triangulation to its information-theoretical limits. Therefore, the line density as well as the measurement depth needs to be significantly increased. This causes serious indexing ambiguities. On the road to a single-shot 3D movie camera, we are working on solutions to overcome the problem of false line indexing by utilizing yet unexploited information. We will present several approaches and will discuss profound information-theoretical questions about the information efficiency of 3D sensors.

  • 4 authors
·
May 17, 2013

Cross-modal feature fusion for robust point cloud registration with ambiguous geometry

Point cloud registration has seen significant advancements with the application of deep learning techniques. However, existing approaches often overlook the potential of integrating radiometric information from RGB images. This limitation reduces their effectiveness in aligning point clouds pairs, especially in regions where geometric data alone is insufficient. When used effectively, radiometric information can enhance the registration process by providing context that is missing from purely geometric data. In this paper, we propose CoFF, a novel Cross-modal Feature Fusion method that utilizes both point cloud geometry and RGB images for pairwise point cloud registration. Assuming that the co-registration between point clouds and RGB images is available, CoFF explicitly addresses the challenges where geometric information alone is unclear, such as in regions with symmetric similarity or planar structures, through a two-stage fusion of 3D point cloud features and 2D image features. It incorporates a cross-modal feature fusion module that assigns pixel-wise image features to 3D input point clouds to enhance learned 3D point features, and integrates patch-wise image features with superpoint features to improve the quality of coarse matching. This is followed by a coarse-to-fine matching module that accurately establishes correspondences using the fused features. We extensively evaluate CoFF on four common datasets: 3DMatch, 3DLoMatch, IndoorLRS, and the recently released ScanNet++ datasets. In addition, we assess CoFF on specific subset datasets containing geometrically ambiguous cases. Our experimental results demonstrate that CoFF achieves state-of-the-art registration performance across all benchmarks, including remarkable registration recalls of 95.9% and 81.6% on the widely-used 3DMatch and 3DLoMatch datasets, respectively...(Truncated to fit arXiv abstract length)

  • 6 authors
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May 19

Multimodal Multitask Representation Learning for Pathology Biobank Metadata Prediction

Metadata are general characteristics of the data in a well-curated and condensed format, and have been proven to be useful for decision making, knowledge discovery, and also heterogeneous data organization of biobank. Among all data types in the biobank, pathology is the key component of the biobank and also serves as the gold standard of diagnosis. To maximize the utility of biobank and allow the rapid progress of biomedical science, it is essential to organize the data with well-populated pathology metadata. However, manual annotation of such information is tedious and time-consuming. In the study, we develop a multimodal multitask learning framework to predict four major slide-level metadata of pathology images. The framework learns generalizable representations across tissue slides, pathology reports, and case-level structured data. We demonstrate improved performance across all four tasks with the proposed method compared to a single modal single task baseline on two test sets, one external test set from a distinct data source (TCGA) and one internal held-out test set (TTH). In the test sets, the performance improvements on the averaged area under receiver operating characteristic curve across the four tasks are 16.48% and 9.05% on TCGA and TTH, respectively. Such pathology metadata prediction system may be adopted to mitigate the effort of expert annotation and ultimately accelerate the data-driven research by better utilization of the pathology biobank.

  • 5 authors
·
Sep 17, 2019

Hoechst Is All You Need: Lymphocyte Classification with Deep Learning

Multiplex immunofluorescence and immunohistochemistry benefit patients by allowing cancer pathologists to identify several proteins expressed on the surface of cells, enabling cell classification, better understanding of the tumour micro-environment, more accurate diagnoses, prognoses, and tailored immunotherapy based on the immune status of individual patients. However, they are expensive and time consuming processes which require complex staining and imaging techniques by expert technicians. Hoechst staining is much cheaper and easier to perform, but is not typically used in this case as it binds to DNA rather than to the proteins targeted by immunofluorescent techniques, and it was not previously thought possible to differentiate cells expressing these proteins based only on DNA morphology. In this work we show otherwise, training a deep convolutional neural network to identify cells expressing three proteins (T lymphocyte markers CD3 and CD8, and the B lymphocyte marker CD20) with greater than 90% precision and recall, from Hoechst 33342 stained tissue only. Our model learns previously unknown morphological features associated with expression of these proteins which can be used to accurately differentiate lymphocyte subtypes for use in key prognostic metrics such as assessment of immune cell infiltration,and thereby predict and improve patient outcomes without the need for costly multiplex immunofluorescence.

  • 4 authors
·
Jul 9, 2021

LLplace: The 3D Indoor Scene Layout Generation and Editing via Large Language Model

Designing 3D indoor layouts is a crucial task with significant applications in virtual reality, interior design, and automated space planning. Existing methods for 3D layout design either rely on diffusion models, which utilize spatial relationship priors, or heavily leverage the inferential capabilities of proprietary Large Language Models (LLMs), which require extensive prompt engineering and in-context exemplars via black-box trials. These methods often face limitations in generalization and dynamic scene editing. In this paper, we introduce LLplace, a novel 3D indoor scene layout designer based on lightweight fine-tuned open-source LLM Llama3. LLplace circumvents the need for spatial relationship priors and in-context exemplars, enabling efficient and credible room layout generation based solely on user inputs specifying the room type and desired objects. We curated a new dialogue dataset based on the 3D-Front dataset, expanding the original data volume and incorporating dialogue data for adding and removing objects. This dataset can enhance the LLM's spatial understanding. Furthermore, through dialogue, LLplace activates the LLM's capability to understand 3D layouts and perform dynamic scene editing, enabling the addition and removal of objects. Our approach demonstrates that LLplace can effectively generate and edit 3D indoor layouts interactively and outperform existing methods in delivering high-quality 3D design solutions. Code and dataset will be released.

  • 7 authors
·
Jun 6, 2024

CellCLIP -- Learning Perturbation Effects in Cell Painting via Text-Guided Contrastive Learning

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

  • 4 authors
·
May 16

3D Copy-Paste: Physically Plausible Object Insertion for Monocular 3D Detection

A major challenge in monocular 3D object detection is the limited diversity and quantity of objects in real datasets. While augmenting real scenes with virtual objects holds promise to improve both the diversity and quantity of the objects, it remains elusive due to the lack of an effective 3D object insertion method in complex real captured scenes. In this work, we study augmenting complex real indoor scenes with virtual objects for monocular 3D object detection. The main challenge is to automatically identify plausible physical properties for virtual assets (e.g., locations, appearances, sizes, etc.) in cluttered real scenes. To address this challenge, we propose a physically plausible indoor 3D object insertion approach to automatically copy virtual objects and paste them into real scenes. The resulting objects in scenes have 3D bounding boxes with plausible physical locations and appearances. In particular, our method first identifies physically feasible locations and poses for the inserted objects to prevent collisions with the existing room layout. Subsequently, it estimates spatially-varying illumination for the insertion location, enabling the immersive blending of the virtual objects into the original scene with plausible appearances and cast shadows. We show that our augmentation method significantly improves existing monocular 3D object models and achieves state-of-the-art performance. For the first time, we demonstrate that a physically plausible 3D object insertion, serving as a generative data augmentation technique, can lead to significant improvements for discriminative downstream tasks such as monocular 3D object detection. Project website: https://gyhandy.github.io/3D-Copy-Paste/

  • 8 authors
·
Dec 8, 2023

PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

  • 22 authors
·
May 16, 2024

Privacy-preserving Pedestrian Tracking using Distributed 3D LiDARs

The growing demand for intelligent environments unleashes an extraordinary cycle of privacy-aware applications that makes individuals' life more comfortable and safe. Examples of these applications include pedestrian tracking systems in large areas. Although the ubiquity of camera-based systems, they are not a preferable solution due to the vulnerability of leaking the privacy of pedestrians. In this paper, we introduce a novel privacy-preserving system for pedestrian tracking in smart environments using multiple distributed LiDARs of non-overlapping views. The system is designed to leverage LiDAR devices to track pedestrians in partially covered areas due to practical constraints, e.g., occlusion or cost. Therefore, the system uses the point cloud captured by different LiDARs to extract discriminative features that are used to train a metric learning model for pedestrian matching purposes. To boost the system's robustness, we leverage a probabilistic approach to model and adapt the dynamic mobility patterns of individuals and thus connect their sub-trajectories. We deployed the system in a large-scale testbed with 70 colorless LiDARs and conducted three different experiments. The evaluation result at the entrance hall confirms the system's ability to accurately track the pedestrians with a 0.98 F-measure even with zero-covered areas. This result highlights the promise of the proposed system as the next generation of privacy-preserving tracking means in smart environments.

  • 5 authors
·
Mar 17, 2023

Learning a Room with the Occ-SDF Hybrid: Signed Distance Function Mingled with Occupancy Aids Scene Representation

Implicit neural rendering, which uses signed distance function (SDF) representation with geometric priors (such as depth or surface normal), has led to impressive progress in the surface reconstruction of large-scale scenes. However, applying this method to reconstruct a room-level scene from images may miss structures in low-intensity areas or small and thin objects. We conducted experiments on three datasets to identify limitations of the original color rendering loss and priors-embedded SDF scene representation. We found that the color rendering loss results in optimization bias against low-intensity areas, causing gradient vanishing and leaving these areas unoptimized. To address this issue, we propose a feature-based color rendering loss that utilizes non-zero feature values to bring back optimization signals. Additionally, the SDF representation can be influenced by objects along a ray path, disrupting the monotonic change of SDF values when a single object is present. To counteract this, we explore using the occupancy representation, which encodes each point separately and is unaffected by objects along a querying ray. Our experimental results demonstrate that the joint forces of the feature-based rendering loss and Occ-SDF hybrid representation scheme can provide high-quality reconstruction results, especially in challenging room-level scenarios. The code would be released.

  • 7 authors
·
Mar 16, 2023

hist2RNA: An efficient deep learning architecture to predict gene expression from breast cancer histopathology images

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is primarily used for ER+ breast cancer, which is costly, tissue destructive, requires specialized platforms and takes several weeks to obtain a result. Deep learning algorithms can effectively extract morphological patterns in digital histopathology images to predict molecular phenotypes quickly and cost-effectively. We propose a new, computationally efficient approach called hist2RNA inspired by bulk RNA-sequencing techniques to predict the expression of 138 genes (incorporated from six commercially available molecular profiling tests), including luminal PAM50 subtype, from hematoxylin and eosin (H&E) stained whole slide images (WSIs). The training phase involves the aggregation of extracted features for each patient from a pretrained model to predict gene expression at the patient level using annotated H&E images from The Cancer Genome Atlas (TCGA, n=335). We demonstrate successful gene prediction on a held-out test set (n = 160, corr = 0.82 across patients, corr = 0.29 across genes) and perform exploratory analysis on an external tissue microarray (TMA) dataset (n = 498) with known IHC and survival information. Our model is able to predict gene expression and luminal PAM50 subtype (Luminal A versus Luminal B) on the TMA dataset with prognostic significance for overall survival in univariate analysis (c-index = 0.56, hazard ratio = 2.16 (95% CI 1.12-3.06), p < 5 x 10-3), and independent significance in multivariate analysis incorporating standard clinicopathological variables (c-index = 0.65, hazard ratio = 1.85 (95% CI 1.30-2.68), p < 5 x 10-3).

  • 6 authors
·
Apr 10, 2023

Phikon-v2, A large and public feature extractor for biomarker prediction

Gathering histopathology slides from over 100 publicly available cohorts, we compile a diverse dataset of 460 million pathology tiles covering more than 30 cancer sites. Using this dataset, we train a large self-supervised vision transformer using DINOv2 and publicly release one iteration of this model for further experimentation, coined Phikon-v2. While trained on publicly available histology slides, Phikon-v2 surpasses our previously released model (Phikon) and performs on par with other histopathology foundation models (FM) trained on proprietary data. Our benchmarks include eight slide-level tasks with results reported on external validation cohorts avoiding any data contamination between pre-training and evaluation datasets. Our downstream training procedure follows a simple yet robust ensembling strategy yielding a +1.75 AUC increase across tasks and models compared to one-shot retraining (p<0.001). We compare Phikon (ViT-B) and Phikon-v2 (ViT-L) against 14 different histology feature extractors, making our evaluation the most comprehensive to date. Our result support evidences that DINOv2 handles joint model and data scaling better than iBOT. Also, we show that recent scaling efforts are overall beneficial to downstream performance in the context of biomarker prediction with GigaPath and H-Optimus-0 (two ViT-g with 1.1B parameters each) standing out. However, the statistical margins between the latest top-performing FMs remain mostly non-significant; some even underperform on specific indications or tasks such as MSI prediction - deposed by a 13x smaller model developed internally. While latest foundation models may exhibit limitations for clinical deployment, they nonetheless offer excellent grounds for the development of more specialized and cost-efficient histology encoders fueling AI-guided diagnostic tools.

  • 4 authors
·
Sep 13, 2024

S-INF: Towards Realistic Indoor Scene Synthesis via Scene Implicit Neural Field

Learning-based methods have become increasingly popular in 3D indoor scene synthesis (ISS), showing superior performance over traditional optimization-based approaches. These learning-based methods typically model distributions on simple yet explicit scene representations using generative models. However, due to the oversimplified explicit representations that overlook detailed information and the lack of guidance from multimodal relationships within the scene, most learning-based methods struggle to generate indoor scenes with realistic object arrangements and styles. In this paper, we introduce a new method, Scene Implicit Neural Field (S-INF), for indoor scene synthesis, aiming to learn meaningful representations of multimodal relationships, to enhance the realism of indoor scene synthesis. S-INF assumes that the scene layout is often related to the object-detailed information. It disentangles the multimodal relationships into scene layout relationships and detailed object relationships, fusing them later through implicit neural fields (INFs). By learning specialized scene layout relationships and projecting them into S-INF, we achieve a realistic generation of scene layout. Additionally, S-INF captures dense and detailed object relationships through differentiable rendering, ensuring stylistic consistency across objects. Through extensive experiments on the benchmark 3D-FRONT dataset, we demonstrate that our method consistently achieves state-of-the-art performance under different types of ISS.

  • 6 authors
·
Dec 23, 2024

DinoBloom: A Foundation Model for Generalizable Cell Embeddings in Hematology

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

  • 8 authors
·
Apr 7, 2024

Enhancing Visual Place Recognition via Fast and Slow Adaptive Biasing in Event Cameras

Event cameras are increasingly popular in robotics due to beneficial features such as low latency, energy efficiency, and high dynamic range. Nevertheless, their downstream task performance is greatly influenced by the optimization of bias parameters. These parameters, for instance, regulate the necessary change in light intensity to trigger an event, which in turn depends on factors such as the environment lighting and camera motion. This paper introduces feedback control algorithms that automatically tune the bias parameters through two interacting methods: 1) An immediate, on-the-fly fast adaptation of the refractory period, which sets the minimum interval between consecutive events, and 2) if the event rate exceeds the specified bounds even after changing the refractory period repeatedly, the controller adapts the pixel bandwidth and event thresholds, which stabilizes after a short period of noise events across all pixels (slow adaptation). Our evaluation focuses on the visual place recognition task, where incoming query images are compared to a given reference database. We conducted comprehensive evaluations of our algorithms' adaptive feedback control in real-time. To do so, we collected the QCR-Fast-and-Slow dataset that contains DAVIS346 event camera streams from 366 repeated traversals of a Scout Mini robot navigating through a 100 meter long indoor lab setting (totaling over 35km distance traveled) in varying brightness conditions with ground truth location information. Our proposed feedback controllers result in superior performance when compared to the standard bias settings and prior feedback control methods. Our findings also detail the impact of bias adjustments on task performance and feature ablation studies on the fast and slow adaptation mechanisms.

  • 3 authors
·
Mar 25, 2024