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Oct 27

SR-CACO-2: A Dataset for Confocal Fluorescence Microscopy Image Super-Resolution

Confocal fluorescence microscopy is one of the most accessible and widely used imaging techniques for the study of biological processes. Scanning confocal microscopy allows the capture of high-quality images from 3D samples, yet suffers from well-known limitations such as photobleaching and phototoxicity of specimens caused by intense light exposure, which limits its use in some applications, especially for living cells. Cellular damage can be alleviated by changing imaging parameters to reduce light exposure, often at the expense of image quality. Machine/deep learning methods for single-image super-resolution (SISR) can be applied to restore image quality by upscaling lower-resolution (LR) images to produce high-resolution images (HR). These SISR methods have been successfully applied to photo-realistic images due partly to the abundance of publicly available data. In contrast, the lack of publicly available data partly limits their application and success in scanning confocal microscopy. In this paper, we introduce a large scanning confocal microscopy dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs marked for three different fluorescent markers. It allows the evaluation of performance of SISR methods on three different upscaling levels (X2, X4, X8). SR-CACO-2 contains the human epithelial cell line Caco-2 (ATCC HTB-37), and it is composed of 22 tiles that have been translated in the form of 9,937 image patches for experiments with SISR methods. Given the new SR-CACO-2 dataset, we also provide benchmarking results for 15 state-of-the-art methods that are representative of the main SISR families. Results show that these methods have limited success in producing high-resolution textures, indicating that SR-CACO-2 represents a challenging problem. Our dataset, code and pretrained weights are available: https://github.com/sbelharbi/sr-caco-2.

  • 6 authors
·
Jun 13, 2024

DISGAN: Wavelet-informed Discriminator Guides GAN to MRI Super-resolution with Noise Cleaning

MRI super-resolution (SR) and denoising tasks are fundamental challenges in the field of deep learning, which have traditionally been treated as distinct tasks with separate paired training data. In this paper, we propose an innovative method that addresses both tasks simultaneously using a single deep learning model, eliminating the need for explicitly paired noisy and clean images during training. Our proposed model is primarily trained for SR, but also exhibits remarkable noise-cleaning capabilities in the super-resolved images. Instead of conventional approaches that introduce frequency-related operations into the generative process, our novel approach involves the use of a GAN model guided by a frequency-informed discriminator. To achieve this, we harness the power of the 3D Discrete Wavelet Transform (DWT) operation as a frequency constraint within the GAN framework for the SR task on magnetic resonance imaging (MRI) data. Specifically, our contributions include: 1) a 3D generator based on residual-in-residual connected blocks; 2) the integration of the 3D DWT with 1times 1 convolution into a DWT+conv unit within a 3D Unet for the discriminator; 3) the use of the trained model for high-quality image SR, accompanied by an intrinsic denoising process. We dub the model "Denoising Induced Super-resolution GAN (DISGAN)" due to its dual effects of SR image generation and simultaneous denoising. Departing from the traditional approach of training SR and denoising tasks as separate models, our proposed DISGAN is trained only on the SR task, but also achieves exceptional performance in denoising. The model is trained on 3D MRI data from dozens of subjects from the Human Connectome Project (HCP) and further evaluated on previously unseen MRI data from subjects with brain tumours and epilepsy to assess its denoising and SR performance.

  • 6 authors
·
Aug 23, 2023

TransRefer3D: Entity-and-Relation Aware Transformer for Fine-Grained 3D Visual Grounding

Recently proposed fine-grained 3D visual grounding is an essential and challenging task, whose goal is to identify the 3D object referred by a natural language sentence from other distractive objects of the same category. Existing works usually adopt dynamic graph networks to indirectly model the intra/inter-modal interactions, making the model difficult to distinguish the referred object from distractors due to the monolithic representations of visual and linguistic contents. In this work, we exploit Transformer for its natural suitability on permutation-invariant 3D point clouds data and propose a TransRefer3D network to extract entity-and-relation aware multimodal context among objects for more discriminative feature learning. Concretely, we devise an Entity-aware Attention (EA) module and a Relation-aware Attention (RA) module to conduct fine-grained cross-modal feature matching. Facilitated by co-attention operation, our EA module matches visual entity features with linguistic entity features while RA module matches pair-wise visual relation features with linguistic relation features, respectively. We further integrate EA and RA modules into an Entity-and-Relation aware Contextual Block (ERCB) and stack several ERCBs to form our TransRefer3D for hierarchical multimodal context modeling. Extensive experiments on both Nr3D and Sr3D datasets demonstrate that our proposed model significantly outperforms existing approaches by up to 10.6% and claims the new state-of-the-art. To the best of our knowledge, this is the first work investigating Transformer architecture for fine-grained 3D visual grounding task.

  • 7 authors
·
Aug 5, 2021

Dense Object Grounding in 3D Scenes

Localizing objects in 3D scenes according to the semantics of a given natural language is a fundamental yet important task in the field of multimedia understanding, which benefits various real-world applications such as robotics and autonomous driving. However, the majority of existing 3D object grounding methods are restricted to a single-sentence input describing an individual object, which cannot comprehend and reason more contextualized descriptions of multiple objects in more practical 3D cases. To this end, we introduce a new challenging task, called 3D Dense Object Grounding (3D DOG), to jointly localize multiple objects described in a more complicated paragraph rather than a single sentence. Instead of naively localizing each sentence-guided object independently, we found that dense objects described in the same paragraph are often semantically related and spatially located in a focused region of the 3D scene. To explore such semantic and spatial relationships of densely referred objects for more accurate localization, we propose a novel Stacked Transformer based framework for 3D DOG, named 3DOGSFormer. Specifically, we first devise a contextual query-driven local transformer decoder to generate initial grounding proposals for each target object. Then, we employ a proposal-guided global transformer decoder that exploits the local object features to learn their correlation for further refining initial grounding proposals. Extensive experiments on three challenging benchmarks (Nr3D, Sr3D, and ScanRefer) show that our proposed 3DOGSFormer outperforms state-of-the-art 3D single-object grounding methods and their dense-object variants by significant margins.

  • 3 authors
·
Sep 5, 2023

3D-SPS: Single-Stage 3D Visual Grounding via Referred Point Progressive Selection

3D visual grounding aims to locate the referred target object in 3D point cloud scenes according to a free-form language description. Previous methods mostly follow a two-stage paradigm, i.e., language-irrelevant detection and cross-modal matching, which is limited by the isolated architecture. In such a paradigm, the detector needs to sample keypoints from raw point clouds due to the inherent properties of 3D point clouds (irregular and large-scale), to generate the corresponding object proposal for each keypoint. However, sparse proposals may leave out the target in detection, while dense proposals may confuse the matching model. Moreover, the language-irrelevant detection stage can only sample a small proportion of keypoints on the target, deteriorating the target prediction. In this paper, we propose a 3D Single-Stage Referred Point Progressive Selection (3D-SPS) method, which progressively selects keypoints with the guidance of language and directly locates the target. Specifically, we propose a Description-aware Keypoint Sampling (DKS) module to coarsely focus on the points of language-relevant objects, which are significant clues for grounding. Besides, we devise a Target-oriented Progressive Mining (TPM) module to finely concentrate on the points of the target, which is enabled by progressive intra-modal relation modeling and inter-modal target mining. 3D-SPS bridges the gap between detection and matching in the 3D visual grounding task, localizing the target at a single stage. Experiments demonstrate that 3D-SPS achieves state-of-the-art performance on both ScanRefer and Nr3D/Sr3D datasets.

  • 8 authors
·
Apr 13, 2022

CoT3DRef: Chain-of-Thoughts Data-Efficient 3D Visual Grounding

3D visual grounding is the ability to localize objects in 3D scenes conditioned by utterances. Most existing methods devote the referring head to localize the referred object directly, causing failure in complex scenarios. In addition, it does not illustrate how and why the network reaches the final decision. In this paper, we address this question Can we design an interpretable 3D visual grounding framework that has the potential to mimic the human perception system?. To this end, we formulate the 3D visual grounding problem as a sequence-to-sequence task by first predicting a chain of anchors and then the final target. Interpretability not only improves the overall performance but also helps us identify failure cases. Following the chain of thoughts approach enables us to decompose the referring task into interpretable intermediate steps, boosting the performance and making our framework extremely data-efficient. Moreover, our proposed framework can be easily integrated into any existing architecture. We validate our approach through comprehensive experiments on the Nr3D, Sr3D, and Scanrefer benchmarks and show consistent performance gains compared to existing methods without requiring manually annotated data. Furthermore, our proposed framework, dubbed CoT3DRef, is significantly data-efficient, whereas on the Sr3D dataset, when trained only on 10% of the data, we match the SOTA performance that trained on the entire data.

  • 5 authors
·
Oct 9, 2023

Distilling Coarse-to-Fine Semantic Matching Knowledge for Weakly Supervised 3D Visual Grounding

3D visual grounding involves finding a target object in a 3D scene that corresponds to a given sentence query. Although many approaches have been proposed and achieved impressive performance, they all require dense object-sentence pair annotations in 3D point clouds, which are both time-consuming and expensive. To address the problem that fine-grained annotated data is difficult to obtain, we propose to leverage weakly supervised annotations to learn the 3D visual grounding model, i.e., only coarse scene-sentence correspondences are used to learn object-sentence links. To accomplish this, we design a novel semantic matching model that analyzes the semantic similarity between object proposals and sentences in a coarse-to-fine manner. Specifically, we first extract object proposals and coarsely select the top-K candidates based on feature and class similarity matrices. Next, we reconstruct the masked keywords of the sentence using each candidate one by one, and the reconstructed accuracy finely reflects the semantic similarity of each candidate to the query. Additionally, we distill the coarse-to-fine semantic matching knowledge into a typical two-stage 3D visual grounding model, which reduces inference costs and improves performance by taking full advantage of the well-studied structure of the existing architectures. We conduct extensive experiments on ScanRefer, Nr3D, and Sr3D, which demonstrate the effectiveness of our proposed method.

  • 8 authors
·
Jul 18, 2023

Chat-3D v2: Bridging 3D Scene and Large Language Models with Object Identifiers

Recent research has evidenced the significant potentials of Large Language Models (LLMs) in handling challenging tasks within 3D scenes. However, current models are constrained to addressing object-centric tasks, where each question-answer pair focuses solely on an individual object. In real-world applications, users may pose queries involving multiple objects or expect for answers that precisely reference various objects. We introduce the use of object identifiers to freely reference objects during a conversation. While this solution appears straightforward, it presents two main challenges: 1) How to establish a reliable one-to-one correspondence between each object and its identifier? 2) How to incorporate complex spatial relationships among dozens of objects into the embedding space of the LLM? To address these challenges, we propose a two-stage alignment method, which involves learning an attribute-aware token and a relation-aware token for each object. These tokens capture the object's attributes and spatial relationships with surrounding objects in the 3D scene. Once the alignment is established, we can fine-tune our model on various downstream tasks using instruction tuning. Experiments conducted on traditional datasets like ScanQA, ScanRefer, and Nr3D/Sr3D showcase the effectiveness of our proposed method. Additionally, we create a 3D scene captioning dataset annotated with rich object identifiers, with the assistant of GPT-4. This dataset aims to further explore the capability of object identifiers in effective object referencing and precise scene understanding.

  • 8 authors
·
Dec 13, 2023

Text-guided Sparse Voxel Pruning for Efficient 3D Visual Grounding

In this paper, we propose an efficient multi-level convolution architecture for 3D visual grounding. Conventional methods are difficult to meet the requirements of real-time inference due to the two-stage or point-based architecture. Inspired by the success of multi-level fully sparse convolutional architecture in 3D object detection, we aim to build a new 3D visual grounding framework following this technical route. However, as in 3D visual grounding task the 3D scene representation should be deeply interacted with text features, sparse convolution-based architecture is inefficient for this interaction due to the large amount of voxel features. To this end, we propose text-guided pruning (TGP) and completion-based addition (CBA) to deeply fuse 3D scene representation and text features in an efficient way by gradual region pruning and target completion. Specifically, TGP iteratively sparsifies the 3D scene representation and thus efficiently interacts the voxel features with text features by cross-attention. To mitigate the affect of pruning on delicate geometric information, CBA adaptively fixes the over-pruned region by voxel completion with negligible computational overhead. Compared with previous single-stage methods, our method achieves top inference speed and surpasses previous fastest method by 100\% FPS. Our method also achieves state-of-the-art accuracy even compared with two-stage methods, with +1.13 lead of [email protected] on ScanRefer, and +2.6 and +3.2 leads on NR3D and SR3D respectively. The code is available at https://github.com/GWxuan/TSP3D{https://github.com/GWxuan/TSP3D}.

  • 6 authors
·
Feb 14 2