Purpose: The recent Segment Anything Model (SAM) has demonstrated impressive performance with point, text or bounding box prompts, in various applications. However, in safety-critical surgical tasks, prompting is not possible due to (i) the lack of per-frame prompts for supervised learning, (ii) it is unrealistic to prompt frame-by-frame in a real-time tracking application, and (iii) it is expensive to annotate prompts for offline applications. Methods: We develop Surgical-DeSAM to generate automatic bounding box prompts for decoupling SAM to obtain instrument segmentation in real-time robotic surgery. We utilise a commonly used detection architecture, DETR, and fine-tuned it to obtain bounding box prompt for the instruments. We then empolyed decoupling SAM (DeSAM) by replacing the image encoder with DETR encoder and fine-tune prompt encoder and mask decoder to obtain instance segmentation for the surgical instruments. To improve detection performance, we adopted the Swin-transformer to better feature representation. Results: The proposed method has been validated on two publicly available datasets from the MICCAI surgical instruments segmentation challenge EndoVis 2017 and 2018. The performance of our method is also compared with SOTA instrument segmentation methods and demonstrated significant improvements with dice metrics of 89.62 and 90.70 for the EndoVis 2017 and 2018. Conclusion: Our extensive experiments and validations demonstrate that Surgical-DeSAM enables real-time instrument segmentation without any additional prompting and outperforms other SOTA segmentation methods.
The future instance prediction from a Bird's Eye View(BEV) perspective is a vital component in autonomous driving, which involves future instance segmentation and instance motion prediction. Existing methods usually rely on a redundant and complex pipeline which requires multiple auxiliary outputs and post-processing procedures. Moreover, estimated errors on each of the auxiliary predictions will lead to degradation of the prediction performance. In this paper, we propose a simple yet effective fully end-to-end framework named Future Instance Prediction Transformer(FipTR), which views the task as BEV instance segmentation and prediction for future frames. We propose to adopt instance queries representing specific traffic participants to directly estimate the corresponding future occupied masks, and thus get rid of complex post-processing procedures. Besides, we devise a flow-aware BEV predictor for future BEV feature prediction composed of a flow-aware deformable attention that takes backward flow guiding the offset sampling. A novel future instance matching strategy is also proposed to further improve the temporal coherence. Extensive experiments demonstrate the superiority of FipTR and its effectiveness under different temporal BEV encoders. The code is available at https://github.com/TabGuigui/FipTR .
Modern agricultural applications rely more and more on deep learning solutions. However, training well-performing deep networks requires a large amount of annotated data that may not be available and in the case of 3D annotation may not even be feasible for human annotators. In this work, we develop a deep learning approach to segment mushrooms and estimate their pose on 3D data, in the form of point clouds acquired by depth sensors. To circumvent the annotation problem, we create a synthetic dataset of mushroom scenes, where we are fully aware of 3D information, such as the pose of each mushroom. The proposed network has a fully convolutional backbone, that parses sparse 3D data, and predicts pose information that implicitly defines both instance segmentation and pose estimation task. We have validated the effectiveness of the proposed implicit-based approach for a synthetic test set, as well as provided qualitative results for a small set of real acquired point clouds with depth sensors. Code is publicly available at https://github.com/georgeretsi/mushroom-pose.
Foundation models, pre-trained on a large amount of data have demonstrated impressive zero-shot capabilities in various downstream tasks. However, in object detection and instance segmentation, two fundamental computer vision tasks heavily reliant on extensive human annotations, foundation models such as SAM and DINO struggle to achieve satisfactory performance. In this study, we reveal that the devil is in the object boundary, \textit{i.e.}, these foundation models fail to discern boundaries between individual objects. For the first time, we probe that CLIP, which has never accessed any instance-level annotations, can provide a highly beneficial and strong instance-level boundary prior in the clustering results of its particular intermediate layer. Following this surprising observation, we propose $\textbf{Zip}$ which $\textbf{Z}$ips up CL$\textbf{ip}$ and SAM in a novel classification-first-then-discovery pipeline, enabling annotation-free, complex-scene-capable, open-vocabulary object detection and instance segmentation. Our Zip significantly boosts SAM's mask AP on COCO dataset by 12.5% and establishes state-of-the-art performance in various settings, including training-free, self-training, and label-efficient finetuning. Furthermore, annotation-free Zip even achieves comparable performance to the best-performing open-vocabulary object detecters using base annotations. Code is released at https://github.com/ChengShiest/Zip-Your-CLIP
The automatic detection of tree-ring boundaries and other anatomical features using image analysis has progressed substantially over the past decade with advances in machine learning and imagery technology, as well as increasing demands from the dendrochronology community. This paper presents a publicly available database of 64 scanned images of transverse sections of commercially grown Pinus taeda trees from northern Uruguay, ranging from 17 to 24 years old. The collection contains several challenging features for automatic ring detection, including illumination and surface preparation variation, fungal infection (blue stains), knot formation, missing cortex or interruptions in outer rings, and radial cracking. This dataset can be used to develop and test automatic tree ring detection algorithms. This paper presents to the dendrochronology community one such method, Cross-Section Tree-Ring Detection (CS-TRD), which identifies and marks complete annual rings in cross-sections for tree species presenting a clear definition between early and latewood. We compare the CS-TRD performance against the ground truth manual delineation of all rings over the UruDendro dataset. The CS-TRD software identified rings with an average F-score of 89% and RMSE error of 5.27px for the entire database in less than 20 seconds per image. Finally, we propose a robust measure of the ring growth using the \emph{equivalent radius} of a circle having the same area enclosed by the detected tree ring. Overall, this study contributes to the dendrochronologist's toolbox of fast and low-cost methods to automatically detect rings in conifer species, particularly for measuring diameter growth rates and stem transverse area using entire cross-sections.
Osteoclast cell image analysis plays a key role in osteoporosis research, but it typically involves extensive manual image processing and hand annotations by a trained expert. In the last few years, a handful of machine learning approaches for osteoclast image analysis have been developed, but none have addressed the full instance segmentation task required to produce the same output as that of the human expert led process. Furthermore, none of the prior, fully automated algorithms have publicly available code, pretrained models, or annotated datasets, inhibiting reproduction and extension of their work. We present a new dataset with ~2*10^5 expert annotated mouse osteoclast masks, together with a deep learning instance segmentation method which works for both in vitro mouse osteoclast cells on plastic tissue culture plates and human osteoclast cells on bone chips. To our knowledge, this is the first work to automate the full osteoclast instance segmentation task. Our method achieves a performance of 0.82 mAP_0.5 (mean average precision at intersection-over-union threshold of 0.5) in cross validation for mouse osteoclasts. We present a novel nuclei-aware osteoclast instance segmentation training strategy (NOISe) based on the unique biology of osteoclasts, to improve the model's generalizability and boost the mAP_0.5 from 0.60 to 0.82 on human osteoclasts. We publish our annotated mouse osteoclast image dataset, instance segmentation models, and code at github.com/michaelwwan/noise to enable reproducibility and to provide a public tool to accelerate osteoporosis research.
We study the problem of self-supervised 3D scene flow estimation from real large-scale raw point cloud sequences, which is crucial to various tasks like trajectory prediction or instance segmentation. In the absence of ground truth scene flow labels, contemporary approaches concentrate on deducing optimizing flow across sequential pairs of point clouds by incorporating structure based regularization on flow and object rigidity. The rigid objects are estimated by a variety of 3D spatial clustering methods. While state-of-the-art methods successfully capture overall scene motion using the Neural Prior structure, they encounter challenges in discerning multi-object motions. We identified the structural constraints and the use of large and strict rigid clusters as the main pitfall of the current approaches and we propose a novel clustering approach that allows for combination of overlapping soft clusters as well as non-overlapping rigid clusters representation. Flow is then jointly estimated with progressively growing non-overlapping rigid clusters together with fixed size overlapping soft clusters. We evaluate our method on multiple datasets with LiDAR point clouds, demonstrating the superior performance over the self-supervised baselines reaching new state of the art results. Our method especially excels in resolving flow in complicated dynamic scenes with multiple independently moving objects close to each other which includes pedestrians, cyclists and other vulnerable road users. Our codes are publicly available on https://github.com/ctu-vras/let-it-flow.
Existing angle-based contour descriptors suffer from lossy representation for non-starconvex shapes. By and large, this is the result of the shape being registered with a single global inner center and a set of radii corresponding to a polar coordinate parameterization. In this paper, we propose AdaContour, an adaptive contour descriptor that uses multiple local representations to desirably characterize complex shapes. After hierarchically encoding object shapes in a training set and constructing a contour matrix of all subdivided regions, we compute a robust low-rank robust subspace and approximate each local contour by linearly combining the shared basis vectors to represent an object. Experiments show that AdaContour is able to represent shapes more accurately and robustly than other descriptors while retaining effectiveness. We validate AdaContour by integrating it into off-the-shelf detectors to enable instance segmentation which demonstrates faithful performance. The code is available at https://github.com/tding1/AdaContour.
CNNs, most notably the UNet, are the default architecture for biomedical segmentation. Transformer-based approaches, such as UNETR, have been proposed to replace them, benefiting from a global field of view, but suffering from larger runtimes and higher parameter counts. The recent Vision Mamba architecture offers a compelling alternative to transformers, also providing a global field of view, but at higher efficiency. Here, we introduce ViM-UNet, a novel segmentation architecture based on it and compare it to UNet and UNETR for two challenging microscopy instance segmentation tasks. We find that it performs similarly or better than UNet, depending on the task, and outperforms UNETR while being more efficient. Our code is open source and documented at https://github.com/constantinpape/torch-em/blob/main/vimunet.md.
Panoptic segmentation, combining semantic and instance segmentation, stands as a cutting-edge computer vision task. Despite recent progress with deep learning models, the dynamic nature of real-world applications necessitates continual learning, where models adapt to new classes (plasticity) over time without forgetting old ones (catastrophic forgetting). Current continual segmentation methods often rely on distillation strategies like knowledge distillation and pseudo-labeling, which are effective but result in increased training complexity and computational overhead. In this paper, we introduce a novel and efficient method for continual panoptic segmentation based on Visual Prompt Tuning, dubbed ECLIPSE. Our approach involves freezing the base model parameters and fine-tuning only a small set of prompt embeddings, addressing both catastrophic forgetting and plasticity and significantly reducing the trainable parameters. To mitigate inherent challenges such as error propagation and semantic drift in continual segmentation, we propose logit manipulation to effectively leverage common knowledge across the classes. Experiments on ADE20K continual panoptic segmentation benchmark demonstrate the superiority of ECLIPSE, notably its robustness against catastrophic forgetting and its reasonable plasticity, achieving a new state-of-the-art. The code is available at https://github.com/clovaai/ECLIPSE.
This paper revives Densely Connected Convolutional Networks (DenseNets) and reveals the underrated effectiveness over predominant ResNet-style architectures. We believe DenseNets' potential was overlooked due to untouched training methods and traditional design elements not fully revealing their capabilities. Our pilot study shows dense connections through concatenation are strong, demonstrating that DenseNets can be revitalized to compete with modern architectures. We methodically refine suboptimal components - architectural adjustments, block redesign, and improved training recipes towards widening DenseNets and boosting memory efficiency while keeping concatenation shortcuts. Our models, employing simple architectural elements, ultimately surpass Swin Transformer, ConvNeXt, and DeiT-III - key architectures in the residual learning lineage. Furthermore, our models exhibit near state-of-the-art performance on ImageNet-1K, competing with the very recent models and downstream tasks, ADE20k semantic segmentation, and COCO object detection/instance segmentation. Finally, we provide empirical analyses that uncover the merits of the concatenation over additive shortcuts, steering a renewed preference towards DenseNet-style designs. Our code is available at https://github.com/naver-ai/rdnet.
Transformers have revolutionized image modeling tasks with adaptations like DeIT, Swin, SVT, Biformer, STVit, and FDVIT. However, these models often face challenges with inductive bias and high quadratic complexity, making them less efficient for high-resolution images. State space models (SSMs) such as Mamba, V-Mamba, ViM, and SiMBA offer an alternative to handle high resolution images in computer vision tasks. These SSMs encounter two major issues. First, they become unstable when scaled to large network sizes. Second, although they efficiently capture global information in images, they inherently struggle with handling local information. To address these challenges, we introduce Heracles, a novel SSM that integrates a local SSM, a global SSM, and an attention-based token interaction module. Heracles leverages a Hartely kernel-based state space model for global image information, a localized convolutional network for local details, and attention mechanisms in deeper layers for token interactions. Our extensive experiments demonstrate that Heracles-C-small achieves state-of-the-art performance on the ImageNet dataset with 84.5\% top-1 accuracy. Heracles-C-Large and Heracles-C-Huge further improve accuracy to 85.9\% and 86.4\%, respectively. Additionally, Heracles excels in transfer learning tasks on datasets such as CIFAR-10, CIFAR-100, Oxford Flowers, and Stanford Cars, and in instance segmentation on the MSCOCO dataset. Heracles also proves its versatility by achieving state-of-the-art results on seven time-series datasets, showcasing its ability to generalize across domains with spectral data, capturing both local and global information. The project page is available at this link.\url{https://github.com/badripatro/heracles}
We present PlainMamba: a simple non-hierarchical state space model (SSM) designed for general visual recognition. The recent Mamba model has shown how SSMs can be highly competitive with other architectures on sequential data and initial attempts have been made to apply it to images. In this paper, we further adapt the selective scanning process of Mamba to the visual domain, enhancing its ability to learn features from two-dimensional images by (i) a continuous 2D scanning process that improves spatial continuity by ensuring adjacency of tokens in the scanning sequence, and (ii) direction-aware updating which enables the model to discern the spatial relations of tokens by encoding directional information. Our architecture is designed to be easy to use and easy to scale, formed by stacking identical PlainMamba blocks, resulting in a model with constant width throughout all layers. The architecture is further simplified by removing the need for special tokens. We evaluate PlainMamba on a variety of visual recognition tasks, achieving performance gains over previous non-hierarchical models and is competitive with hierarchical alternatives. For tasks requiring high-resolution inputs, in particular, PlainMamba requires much less computing while maintaining high performance. Code and models are available at: https://github.com/ChenhongyiYang/PlainMamba .
Recently, progress in acquisition equipment such as LiDAR sensors has enabled sensing increasingly spacious outdoor 3D environments. Making sense of such 3D acquisitions requires fine-grained scene understanding, such as constructing instance-based 3D scene segmentations. Commonly, a neural network is trained for this task; however, this requires access to a large, densely annotated dataset, which is widely known to be challenging to obtain. To address this issue, in this work we propose to predict instance segmentations for 3D scenes in an unsupervised way, without relying on ground-truth annotations. To this end, we construct a learning framework consisting of two components: (1) a pseudo-annotation scheme for generating initial unsupervised pseudo-labels; and (2) a self-training algorithm for instance segmentation to fit robust, accurate instances from initial noisy proposals. To enable generating 3D instance mask proposals, we construct a weighted proxy-graph by connecting 3D points with edges integrating multi-modal image- and point-based self-supervised features, and perform graph-cuts to isolate individual pseudo-instances. We then build on a state-of-the-art point-based architecture and train a 3D instance segmentation model, resulting in significant refinement of initial proposals. To scale to arbitrary complexity 3D scenes, we design our algorithm to operate on local 3D point chunks and construct a merging step to generate scene-level instance segmentations. Experiments on the challenging SemanticKITTI benchmark demonstrate the potential of our approach, where it attains 13.3% higher Average Precision and 9.1% higher F1 score compared to the best-performing baseline. The code will be made publicly available at https://github.com/artonson/autoinst.
3D instance segmentation (3DIS) is a crucial task, but point-level annotations are tedious in fully supervised settings. Thus, using bounding boxes (bboxes) as annotations has shown great potential. The current mainstream approach is a two-step process, involving the generation of pseudo-labels from box annotations and the training of a 3DIS network with the pseudo-labels. However, due to the presence of intersections among bboxes, not every point has a determined instance label, especially in overlapping areas. To generate higher quality pseudo-labels and achieve more precise weakly supervised 3DIS results, we propose the Box-Supervised Simulation-assisted Mean Teacher for 3D Instance Segmentation (BSNet), which devises a novel pseudo-labeler called Simulation-assisted Transformer. The labeler consists of two main components. The first is Simulation-assisted Mean Teacher, which introduces Mean Teacher for the first time in this task and constructs simulated samples to assist the labeler in acquiring prior knowledge about overlapping areas. To better model local-global structure, we also propose Local-Global Aware Attention as the decoder for teacher and student labelers. Extensive experiments conducted on the ScanNetV2 and S3DIS datasets verify the superiority of our designs. Code is available at \href{https://github.com/peoplelu/BSNet}{https://github.com/peoplelu/BSNet}.
Foundation models have reshaped the landscape of Remote Sensing (RS) by enhancing various image interpretation tasks. Pretraining is an active research topic, encompassing supervised and self-supervised learning methods to initialize model weights effectively. However, transferring the pretrained models to downstream tasks may encounter task discrepancy due to their formulation of pretraining as image classification or object discrimination tasks. In this study, we explore the Multi-Task Pretraining (MTP) paradigm for RS foundation models to address this issue. Using a shared encoder and task-specific decoder architecture, we conduct multi-task supervised pretraining on the SAMRS dataset, encompassing semantic segmentation, instance segmentation, and rotated object detection. MTP supports both convolutional neural networks and vision transformer foundation models with over 300 million parameters. The pretrained models are finetuned on various RS downstream tasks, such as scene classification, horizontal and rotated object detection, semantic segmentation, and change detection. Extensive experiments across 14 datasets demonstrate the superiority of our models over existing ones of similar size and their competitive performance compared to larger state-of-the-art models, thus validating the effectiveness of MTP.
Open-vocabulary video instance segmentation strives to segment and track instances belonging to an open set of categories in a videos. The vision-language model Contrastive Language-Image Pre-training (CLIP) has shown robust zero-shot classification ability in image-level open-vocabulary tasks. In this paper, we propose a simple encoder-decoder network, called CLIP-VIS, to adapt CLIP for open-vocabulary video instance segmentation. Our CLIP-VIS adopts frozen CLIP and introduces three modules, including class-agnostic mask generation, temporal topK-enhanced matching, and weighted open-vocabulary classification. Given a set of initial queries, class-agnostic mask generation introduces a pixel decoder and a transformer decoder on CLIP pre-trained image encoder to predict query masks and corresponding object scores and mask IoU scores. Then, temporal topK-enhanced matching performs query matching across frames using the K mostly matched frames. Finally, weighted open-vocabulary classification first employs mask pooling to generate query visual features from CLIP pre-trained image encoder, and second performs weighted classification using object scores and mask IoU scores. Our CLIP-VIS does not require the annotations of instance categories and identities. The experiments are performed on various video instance segmentation datasets, which demonstrate the effectiveness of our proposed method, especially for novel categories. When using ConvNeXt-B as backbone, our CLIP-VIS achieves the AP and APn scores of 32.2% and 40.2% on the validation set of LV-VIS dataset, which outperforms OV2Seg by 11.1% and 23.9% respectively. We will release the source code and models at https://github.com/zwq456/CLIP-VIS.git.
We present a neural radiance field method for urban-scale semantic and building-level instance segmentation from aerial images by lifting noisy 2D labels to 3D. This is a challenging problem due to two primary reasons. Firstly, objects in urban aerial images exhibit substantial variations in size, including buildings, cars, and roads, which pose a significant challenge for accurate 2D segmentation. Secondly, the 2D labels generated by existing segmentation methods suffer from the multi-view inconsistency problem, especially in the case of aerial images, where each image captures only a small portion of the entire scene. To overcome these limitations, we first introduce a scale-adaptive semantic label fusion strategy that enhances the segmentation of objects of varying sizes by combining labels predicted from different altitudes, harnessing the novel-view synthesis capabilities of NeRF. We then introduce a novel cross-view instance label grouping strategy based on the 3D scene representation to mitigate the multi-view inconsistency problem in the 2D instance labels. Furthermore, we exploit multi-view reconstructed depth priors to improve the geometric quality of the reconstructed radiance field, resulting in enhanced segmentation results. Experiments on multiple real-world urban-scale datasets demonstrate that our approach outperforms existing methods, highlighting its effectiveness.
Amodal Instance Segmentation (AIS) presents a challenging task as it involves predicting both visible and occluded parts of objects within images. Existing AIS methods rely on a bidirectional approach, encompassing both the transition from amodal features to visible features (amodal-to-visible) and from visible features to amodal features (visible-to-amodal). Our observation shows that the utilization of amodal features through the amodal-to-visible can confuse the visible features due to the extra information of occluded/hidden segments not presented in visible display. Consequently, this compromised quality of visible features during the subsequent visible-to-amodal transition. To tackle this issue, we introduce ShapeFormer, a decoupled Transformer-based model with a visible-to-amodal transition. It facilitates the explicit relationship between output segmentations and avoids the need for amodal-to-visible transitions. ShapeFormer comprises three key modules: (i) Visible-Occluding Mask Head for predicting visible segmentation with occlusion awareness, (ii) Shape-Prior Amodal Mask Head for predicting amodal and occluded masks, and (iii) Category-Specific Shape Prior Retriever aims to provide shape prior knowledge. Comprehensive experiments and extensive ablation studies across various AIS benchmarks demonstrate the effectiveness of our ShapeFormer. The code is available at: \url{https://github.com/UARK-AICV/ShapeFormer}
Stain normalization algorithms aim to transform the color and intensity characteristics of a source multi-gigapixel histology image to match those of a target image, mitigating inconsistencies in the appearance of stains used to highlight cellular components in the images. We propose a new approach, StainFuser, which treats this problem as a style transfer task using a novel Conditional Latent Diffusion architecture, eliminating the need for handcrafted color components. With this method, we curate SPI-2M the largest stain normalization dataset to date of over 2 million histology images with neural style transfer for high-quality transformations. Trained on this data, StainFuser outperforms current state-of-the-art deep learning and handcrafted methods in terms of the quality of normalized images and in terms of downstream model performance on the CoNIC dataset.