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.
Labeling pixel-wise object masks in videos is a resource-intensive and laborious process. Box-supervised Video Instance Segmentation (VIS) methods have emerged as a viable solution to mitigate the labor-intensive annotation process. . In practical applications, the two-step approach is not only more flexible but also exhibits a higher recognition accuracy. Inspired by the recent success of Segment Anything Model (SAM), we introduce a novel approach that aims at harnessing instance box annotations from multiple perspectives to generate high-quality instance pseudo masks, thus enriching the information contained in instance annotations. We leverage ground-truth boxes to create three types of pseudo masks using the HQ-SAM model, the box-supervised VIS model (IDOL-BoxInst), and the VOS model (DeAOT) separately, along with three corresponding optimization mechanisms. Additionally, we introduce two ground-truth data filtering methods, assisted by high-quality pseudo masks, to further enhance the training dataset quality and improve the performance of fully supervised VIS methods. To fully capitalize on the obtained high-quality Pseudo Masks, we introduce a novel algorithm, PM-VIS, to integrate mask losses into IDOL-BoxInst. Our PM-VIS model, trained with high-quality pseudo mask annotations, demonstrates strong ability in instance mask prediction, achieving state-of-the-art performance on the YouTube-VIS 2019, YouTube-VIS 2021, and OVIS validation sets, notably narrowing the gap between box-supervised and fully supervised VIS methods.
Nuclei instance segmentation is crucial in oncological diagnosis and cancer pathology research. H&E stained images are commonly used for medical diagnosis, but pre-processing is necessary before using them for image processing tasks. Two principal pre-processing methods are formalin-fixed paraffin-embedded samples (FFPE) and frozen tissue samples (FS). While FFPE is widely used, it is time-consuming, while FS samples can be processed quickly. Analyzing H&E stained images derived from fast sample preparation, staining, and scanning can pose difficulties due to the swift process, which can result in the degradation of image quality. This paper proposes a method that leverages the unique optical characteristics of H&E stained images. A three-branch U-Net architecture has been implemented, where each branch contributes to the final segmentation results. The process includes applying watershed algorithm to separate overlapping regions and enhance accuracy. The Triple U-Net architecture comprises an RGB branch, a Hematoxylin branch, and a Segmentation branch. This study focuses on a novel dataset named CryoNuSeg. The results obtained through robust experiments outperform the state-of-the-art results across various metrics. The benchmark score for this dataset is AJI 52.5 and PQ 47.7, achieved through the implementation of U-Net Architecture. However, the proposed Triple U-Net architecture achieves an AJI score of 67.41 and PQ of 50.56. The proposed architecture improves more on AJI than other evaluation metrics, which further justifies the superiority of the Triple U-Net architecture over the baseline U-Net model, as AJI is a more strict evaluation metric. The use of the three-branch U-Net model, followed by watershed post-processing, significantly surpasses the benchmark scores, showing substantial improvement in the AJI score
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 .
In recent years, modern techniques in deep learning and large-scale datasets have led to impressive progress in 3D instance segmentation, grasp pose estimation, and robotics. This allows for accurate detection directly in 3D scenes, object- and environment-aware grasp prediction, as well as robust and repeatable robotic manipulation. This work aims to integrate these recent methods into a comprehensive framework for robotic interaction and manipulation in human-centric environments. Specifically, we leverage 3D reconstructions from a commodity 3D scanner for open-vocabulary instance segmentation, alongside grasp pose estimation, to demonstrate dynamic picking of objects, and opening of drawers. We show the performance and robustness of our model in two sets of real-world experiments including dynamic object retrieval and drawer opening, reporting a 51% and 82% success rate respectively. Code of our framework as well as videos are available on: https://spot-compose.github.io/.
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.
The Segment Anything Model (SAM) is a deep neural network foundational model designed to perform instance segmentation which has gained significant popularity given its zero-shot segmentation ability. SAM operates by generating masks based on various input prompts such as text, bounding boxes, points, or masks, introducing a novel methodology to overcome the constraints posed by dataset-specific scarcity. While SAM is trained on an extensive dataset, comprising ~11M images, it mostly consists of natural photographic images with only very limited images from other modalities. Whilst the rapid progress in visual infrared surveillance and X-ray security screening imaging technologies, driven forward by advances in deep learning, has significantly enhanced the ability to detect, classify and segment objects with high accuracy, it is not evident if the SAM zero-shot capabilities can be transferred to such modalities. This work assesses SAM capabilities in segmenting objects of interest in the X-ray/infrared modalities. Our approach reuses the pre-trained SAM with three different prompts: bounding box, centroid and random points. We present quantitative/qualitative results to showcase the performance on selected datasets. Our results show that SAM can segment objects in the X-ray modality when given a box prompt, but its performance varies for point prompts. Specifically, SAM performs poorly in segmenting slender objects and organic materials, such as plastic bottles. We find that infrared objects are also challenging to segment with point prompts given the low-contrast nature of this modality. This study shows that while SAM demonstrates outstanding zero-shot capabilities with box prompts, its performance ranges from moderate to poor for point prompts, indicating that special consideration on the cross-modal generalisation of SAM is needed when considering use on X-ray/infrared imagery.
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 operating environment of a highly automated vehicle is subject to change, e.g., weather, illumination, or the scenario containing different objects and other participants in which the highly automated vehicle has to navigate its passengers safely. These situations must be considered when developing and validating highly automated driving functions. This already poses a problem for training and evaluating deep learning models because without the costly labeling of thousands of recordings, not knowing whether the data contains relevant, interesting data for further model training, it is a guess under which conditions and situations the model performs poorly. For this purpose, we present corner case criteria based on the predictive uncertainty. With our corner case criteria, we are able to detect uncertainty-based corner cases of an object instance segmentation model without relying on ground truth (GT) data. We evaluated each corner case criterion using the COCO and the NuImages dataset to analyze the potential of our approach. We also provide a corner case decision function that allows us to distinguish each object into True Positive (TP), localization and/or classification corner case, or False Positive (FP). We also present our first results of an iterative training cycle that outperforms the baseline and where the data added to the training dataset is selected based on the corner case decision function.
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.
Recent years have seen significant efforts to adopt Artificial Intelligence (AI) in healthcare for various use cases, from computer-aided diagnosis to ICU triage. However, the size of AI models has been rapidly growing due to scaling laws and the success of foundational models, which poses an increasing challenge to leverage advanced models in practical applications. It is thus imperative to develop efficient models, especially for deploying AI solutions under resource-constrains or with time sensitivity. One potential solution is to perform model compression, a set of techniques that remove less important model components or reduce parameter precision, to reduce model computation demand. In this work, we demonstrate that model pruning, as a model compression technique, can effectively reduce inference cost for computational and digital pathology based analysis with a negligible loss of analysis performance. To this end, we develop a methodology for pruning the widely used U-Net-style architectures in biomedical imaging, with which we evaluate multiple pruning heuristics on nuclei instance segmentation and classification, and empirically demonstrate that pruning can compress models by at least 70% with a negligible drop in performance.
Cell segmentation is essential in biomedical research for analyzing cellular morphology and behavior. Deep learning methods, particularly convolutional neural networks (CNNs), have revolutionized cell segmentation by extracting intricate features from images. However, the robustness of these methods under microscope optical aberrations remains a critical challenge. This study evaluates cell image segmentation models under optical aberrations from fluorescence and bright field microscopy. By simulating different types of aberrations, including astigmatism, coma, spherical aberration, trefoil, and mixed aberrations, we conduct a thorough evaluation of various cell instance segmentation models using the DynamicNuclearNet (DNN) and LIVECell datasets, representing fluorescence and bright field microscopy cell datasets, respectively. We train and test several segmentation models, including the Otsu threshold method and Mask R-CNN with different network heads (FPN, C3) and backbones (ResNet, VGG, Swin Transformer), under aberrated conditions. Additionally, we provide usage recommendations for the Cellpose 2.0 Toolbox on complex cell degradation images. The results indicate that the combination of FPN and SwinS demonstrates superior robustness in handling simple cell images affected by minor aberrations. In contrast, Cellpose 2.0 proves effective for complex cell images under similar conditions. Furthermore, we innovatively propose the Point Spread Function Image Label Classification Model (PLCM). This model can quickly and accurately identify aberration types and amplitudes from PSF images, assisting researchers without optical training. Through PLCM, researchers can better apply our proposed cell segmentation guidelines.
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.
Developing countries usually lack the proper governance means to generate and regularly update a national rooftop map. Using traditional photogrammetry and surveying methods to produce a building map at the federal level is costly and time consuming. Using earth observation and deep learning methods, we can bridge this gap and propose an automated pipeline to fetch such national urban maps. This paper aims to exploit the power of fully convolutional neural networks for multi-class buildings' instance segmentation to leverage high object-wise accuracy results. Buildings' instance segmentation from sub-meter high-resolution satellite images can be achieved with relatively high pixel-wise metric scores. We detail all engineering steps to replicate this work and ensure highly accurate results in dense and slum areas witnessed in regions that lack proper urban planning in the Global South. We applied a case study of the proposed pipeline to Lebanon and successfully produced the first comprehensive national building footprint map with approximately 1 Million units with an 84% accuracy. The proposed architecture relies on advanced augmentation techniques to overcome dataset scarcity, which is often the case in developing countries.
Current remote-sensing interpretation models often focus on a single task such as detection, segmentation, or caption. However, the task-specific designed models are unattainable to achieve the comprehensive multi-level interpretation of images. The field also lacks support for multi-task joint interpretation datasets. In this paper, we propose Panoptic Perception, a novel task and a new fine-grained dataset (FineGrip) to achieve a more thorough and universal interpretation for RSIs. The new task, 1) integrates pixel-level, instance-level, and image-level information for universal image perception, 2) captures image information from coarse to fine granularity, achieving deeper scene understanding and description, and 3) enables various independent tasks to complement and enhance each other through multi-task learning. By emphasizing multi-task interactions and the consistency of perception results, this task enables the simultaneous processing of fine-grained foreground instance segmentation, background semantic segmentation, and global fine-grained image captioning. Concretely, the FineGrip dataset includes 2,649 remote sensing images, 12,054 fine-grained instance segmentation masks belonging to 20 foreground things categories, 7,599 background semantic masks for 5 stuff classes and 13,245 captioning sentences. Furthermore, we propose a joint optimization-based panoptic perception model. Experimental results on FineGrip demonstrate the feasibility of the panoptic perception task and the beneficial effect of multi-task joint optimization on individual tasks. The dataset will be publicly available.
The increasing relevance of panoptic segmentation is tied to the advancements in autonomous driving and AR/VR applications. However, the deployment of such models has been limited due to the expensive nature of dense data annotation, giving rise to unsupervised domain adaptation (UDA). A key challenge in panoptic UDA is reducing the domain gap between a labeled source and an unlabeled target domain while harmonizing the subtasks of semantic and instance segmentation to limit catastrophic interference. While considerable progress has been achieved, existing approaches mainly focus on the adaptation of semantic segmentation. In this work, we focus on incorporating instance-level adaptation via a novel instance-aware cross-domain mixing strategy IMix. IMix significantly enhances the panoptic quality by improving instance segmentation performance. Specifically, we propose inserting high-confidence predicted instances from the target domain onto source images, retaining the exhaustiveness of the resulting pseudo-labels while reducing the injected confirmation bias. Nevertheless, such an enhancement comes at the cost of degraded semantic performance, attributed to catastrophic forgetting. To mitigate this issue, we regularize our semantic branch by employing CLIP-based domain alignment (CDA), exploiting the domain-robustness of natural language prompts. Finally, we present an end-to-end model incorporating these two mechanisms called LIDAPS, achieving state-of-the-art results on all popular panoptic UDA benchmarks.
Numerous roadside perception datasets have been introduced to propel advancements in autonomous driving and intelligent transportation systems research and development. However, it has been observed that the majority of their concentrates is on urban arterial roads, inadvertently overlooking residential areas such as parks and campuses that exhibit entirely distinct characteristics. In light of this gap, we propose CORP, which stands as the first public benchmark dataset tailored for multi-modal roadside perception tasks under campus scenarios. Collected in a university campus, CORP consists of over 205k images plus 102k point clouds captured from 18 cameras and 9 LiDAR sensors. These sensors with different configurations are mounted on roadside utility poles to provide diverse viewpoints within the campus region. The annotations of CORP encompass multi-dimensional information beyond 2D and 3D bounding boxes, providing extra support for 3D seamless tracking and instance segmentation with unique IDs and pixel masks for identifying targets, to enhance the understanding of objects and their behaviors distributed across the campus premises. Unlike other roadside datasets about urban traffic, CORP extends the spectrum to highlight the challenges for multi-modal perception in campuses and other residential areas.