Pre-training & fine-tuning can enhance the transferring efficiency and performance in visual tasks. Recent delta-tuning methods provide more options for visual classification tasks. Despite their success, existing visual delta-tuning art fails to exceed the upper limit of full fine-tuning on challenging tasks like object detection and segmentation. To find a competitive alternative to full fine-tuning, we propose the Multi-cognitive Visual Adapter (Mona) tuning, a novel adapter-based tuning method. First, we introduce multiple vision-friendly filters into the adapter to enhance its ability to process visual signals, while previous methods mainly rely on language-friendly linear filters. Second, we add the scaled normalization layer in the adapter to regulate the distribution of input features for visual filters. To fully demonstrate the practicality and generality of Mona, we conduct experiments on multiple representative visual tasks, including instance segmentation on COCO, semantic segmentation on ADE20K, object detection on Pascal VOC, oriented object detection on DOTA/STAR, and image classification on three common datasets. Exciting results illustrate that Mona surpasses full fine-tuning on all these tasks, and is the only delta-tuning method outperforming full fine-tuning on the above various tasks. For example, Mona achieves 1% performance gain on the COCO dataset compared to full fine-tuning. Comprehensive results suggest that Mona-tuning is more suitable for retaining and utilizing the capabilities of pre-trained models than full fine-tuning. The code will be released at https://github.com/Leiyi-Hu/mona.
Cell nuclei instance segmentation is a crucial task in digital kidney pathology. Traditional automatic segmentation methods often lack generalizability when applied to unseen datasets. Recently, the success of foundation models (FMs) has provided a more generalizable solution, potentially enabling the segmentation of any cell type. In this study, we perform a large-scale evaluation of three widely used state-of-the-art (SOTA) cell nuclei foundation models (Cellpose, StarDist, and CellViT). Specifically, we created a highly diverse evaluation dataset consisting of 2,542 kidney whole slide images (WSIs) collected from both human and rodent sources, encompassing various tissue types, sizes, and staining methods. To our knowledge, this is the largest-scale evaluation of its kind to date. Our quantitative analysis of the prediction distribution reveals a persistent performance gap in kidney pathology. Among the evaluated models, CellViT demonstrated superior performance in segmenting nuclei in kidney pathology. However, none of the foundation models are perfect; a performance gap remains in general nuclei segmentation for kidney pathology.
Accurate identification of strawberries during their maturing stages is crucial for optimizing yield management, and pest control, and making informed decisions related to harvest and post-harvest logistics. This study evaluates the performance of YOLOv8 model configurations for instance segmentation of strawberries into ripe and unripe stages in an open field environment. The YOLOv8n model demonstrated superior segmentation accuracy with a mean Average Precision (mAP) of 80.9\%, outperforming other YOLOv8 configurations. In terms of inference speed, YOLOv8n processed images at 12.9 milliseconds, while YOLOv8s, the least-performing model, processed at 22.2 milliseconds. Over 86 test images with 348 ground truth labels, YOLOv8n detected 235 ripe fruit classes and 51 unripe fruit classes out of 251 ground truth ripe fruits and 97 unripe ground truth labels, respectively. In comparison, YOLOv8s detected 204 ripe fruits and 37 unripe fruits. Overall, YOLOv8n achieved the fastest inference speed of 24.2 milliseconds, outperforming YOLOv8s, YOLOv8m, YOLOv8l, and YOLOv8x, which processed images at 33.0 milliseconds, 44.3 milliseconds, 53.6 milliseconds, and 62.5 milliseconds, respectively. These results underscore the potential of advanced object segmentation algorithms to address complex visual recognition tasks in open-field agriculture effectively to address complex visual recognition tasks in open-field agriculture effectively.
We introduce uncertainty-aware object instance segmentation (UncOS) and demonstrate its usefulness for embodied interactive segmentation. To deal with uncertainty in robot perception, we propose a method for generating a hypothesis distribution of object segmentation. We obtain a set of region-factored segmentation hypotheses together with confidence estimates by making multiple queries of large pre-trained models. This process can produce segmentation results that achieve state-of-the-art performance on unseen object segmentation problems. The output can also serve as input to a belief-driven process for selecting robot actions to perturb the scene to reduce ambiguity. We demonstrate the effectiveness of this method in real-robot experiments. Website: https://sites.google.com/view/embodied-uncertain-seg
Live-cell microscopy allows to go beyond measuring average features of cellular populations to observe, quantify and explain biological heterogeneity. Deep Learning-based instance segmentation and cell tracking form the gold standard analysis tools to process the microscopy data collected, but tracking in particular suffers severely from low temporal resolution. In this work, we show that approximating cell cycle time distributions in microbial colonies of C. glutamicum is possible without performing tracking, even at low temporal resolution. To this end, we infer the parameters of a stochastic multi-stage birth process model using the Bayesian Synthetic Likelihood method at varying temporal resolutions by subsampling microscopy sequences, for which ground truth tracking is available. Our results indicate, that the proposed approach yields high quality approximations even at very low temporal resolution, where tracking fails to yield reasonable results.
Vision Transformers (ViTs) mark a revolutionary advance in neural networks with their token mixer's powerful global context capability. However, the pairwise token affinity and complex matrix operations limit its deployment on resource-constrained scenarios and real-time applications, such as mobile devices, although considerable efforts have been made in previous works. In this paper, we introduce CAS-ViT: Convolutional Additive Self-attention Vision Transformers, to achieve a balance between efficiency and performance in mobile applications. Firstly, we argue that the capability of token mixers to obtain global contextual information hinges on multiple information interactions, such as spatial and channel domains. Subsequently, we propose Convolutional Additive Token Mixer (CATM) employing underlying spatial and channel attention as novel interaction forms. This module eliminates troublesome complex operations such as matrix multiplication and Softmax. We introduce Convolutional Additive Self-attention(CAS) block hybrid architecture and utilize CATM for each block. And further, we build a family of lightweight networks, which can be easily extended to various downstream tasks. Finally, we evaluate CAS-ViT across a variety of vision tasks, including image classification, object detection, instance segmentation, and semantic segmentation. Our M and T model achieves 83.0\%/84.1\% top-1 with only 12M/21M parameters on ImageNet-1K. Meanwhile, throughput evaluations on GPUs, ONNX, and iPhones also demonstrate superior results compared to other state-of-the-art backbones. Extensive experiments demonstrate that our approach achieves a better balance of performance, efficient inference and easy-to-deploy. Our code and model are available at: \url{https://github.com/Tianfang-Zhang/CAS-ViT}
The semantic segmentation task in pathology plays an indispensable role in assisting physicians in determining the condition of tissue lesions. With the proposal of Segment Anything Model (SAM), more and more foundation models have seen rapid development in the field of image segmentation. Recently, SAM2 has garnered widespread attention in both natural image and medical image segmentation. Compared to SAM, it has significantly improved in terms of segmentation accuracy and generalization performance. We compared the foundational models based on SAM and found that their performance in semantic segmentation of pathological images was hardly satisfactory. In this paper, we propose Path-SAM2, which for the first time adapts the SAM2 model to cater to the task of pathological semantic segmentation. We integrate the largest pretrained vision encoder for histopathology (UNI) with the original SAM2 encoder, adding more pathology-based prior knowledge. Additionally, we introduce a learnable Kolmogorov-Arnold Networks (KAN) classification module to replace the manual prompt process. In three adenoma pathological datasets, Path-SAM2 has achieved state-of-the-art performance.This study demonstrates the great potential of adapting SAM2 to pathology image segmentation tasks. We plan to release the code and model weights for this paper at: https://github.com/simzhangbest/SAM2PATH
With breakthroughs in large-scale modeling, the Segment Anything Model (SAM) and its extensions have been attempted for applications in various underwater visualization tasks in marine sciences, and have had a significant impact on the academic community. Recently, Meta has further developed the Segment Anything Model 2 (SAM2), which significantly improves running speed and segmentation accuracy compared to its predecessor. This report aims to explore the potential of SAM2 in marine science by evaluating it on the underwater instance segmentation benchmark datasets UIIS and USIS10K. The experiments show that the performance of SAM2 is extremely dependent on the type of user-provided prompts. When using the ground truth bounding box as prompt, SAM2 performed excellently in the underwater instance segmentation domain. However, when running in automatic mode, SAM2's ability with point prompts to sense and segment underwater instances is significantly degraded. It is hoped that this paper will inspire researchers to further explore the SAM model family in the underwater domain. The results and evaluation codes in this paper are available at https://github.com/LiamLian0727/UnderwaterSAM2Eval.
In pathology, accurate and efficient analysis of Hematoxylin and Eosin (H\&E) slides is crucial for timely and effective cancer diagnosis. Although many deep learning solutions for nuclei instance segmentation and classification exist in the literature, they often entail high computational costs and resource requirements, thus limiting their practical usage in medical applications. To address this issue, we introduce a novel convolutional neural network, NuLite, a U-Net-like architecture designed explicitly on Fast-ViT, a state-of-the-art (SOTA) lightweight CNN. We obtained three versions of our model, NuLite-S, NuLite-M, and NuLite-H, trained on the PanNuke dataset. The experimental results prove that our models equal CellViT (SOTA) in terms of panoptic quality and detection. However, our lightest model, NuLite-S, is 40 times smaller in terms of parameters and about 8 times smaller in terms of GFlops, while our heaviest model is 17 times smaller in terms of parameters and about 7 times smaller in terms of GFlops. Moreover, our model is up to about 8 times faster than CellViT. Lastly, to prove the effectiveness of our solution, we provide a robust comparison of external datasets, namely CoNseP, MoNuSeg, and GlySAC. Our model is publicly available at https://github.com/CosmoIknosLab/NuLite
Segmentation of surgical instruments is crucial for enhancing surgeon performance and ensuring patient safety. Conventional techniques such as binary, semantic, and instance segmentation share a common drawback: they do not accommodate the parts of instruments obscured by tissues or other instruments. Precisely predicting the full extent of these occluded instruments can significantly improve laparoscopic surgeries by providing critical guidance during operations and assisting in the analysis of potential surgical errors, as well as serving educational purposes. In this paper, we introduce Amodal Segmentation to the realm of surgical instruments in the medical field. This technique identifies both the visible and occluded parts of an object. To achieve this, we introduce a new Amoal Instruments Segmentation (AIS) dataset, which was developed by reannotating each instrument with its complete mask, utilizing the 2017 MICCAI EndoVis Robotic Instrument Segmentation Challenge dataset. Additionally, we evaluate several leading amodal segmentation methods to establish a benchmark for this new dataset.
In computer vision, it is well-known that a lack of data diversity will impair model performance. In this study, we address the challenges of enhancing the dataset diversity problem in order to benefit various downstream tasks such as object detection and instance segmentation. We propose a simple yet effective data augmentation approach by leveraging advancements in generative models, specifically text-to-image synthesis technologies like Stable Diffusion. Our method focuses on generating variations of labeled real images, utilizing generative object and background augmentation via inpainting to augment existing training data without the need for additional annotations. We find that background augmentation, in particular, significantly improves the models' robustness and generalization capabilities. We also investigate how to adjust the prompt and mask to ensure the generated content comply with the existing annotations. The efficacy of our augmentation techniques is validated through comprehensive evaluations of the COCO dataset and several other key object detection benchmarks, demonstrating notable enhancements in model performance across diverse scenarios. This approach offers a promising solution to the challenges of dataset enhancement, contributing to the development of more accurate and robust computer vision models.
Instance segmentation is an advanced form of image segmentation which, beyond traditional segmentation, requires identifying individual instances of repeating objects in a scene. Mask R-CNN is the most common architecture for instance segmentation, and improvements to this architecture include steps such as benefiting from bounding box refinements, adding semantics, or backbone enhancements. In all the proposed variations to date, the problem of competing kernels (each class aims to maximize its own accuracy) persists when models try to synchronously learn numerous classes. In this paper, we propose mitigating this problem by replacing mask prediction with a Switch-Split block that processes refined ROIs, classifies them, and assigns them to specialized mask predictors. We name the method MaskUno and test it on various models from the literature, which are then trained on multiple classes using the benchmark COCO dataset. An increase in the mean Average Precision (mAP) of 2.03% was observed for the high-performing DetectoRS when trained on 80 classes. MaskUno proved to enhance the mAP of instance segmentation models regardless of the number and typ
Digital Reconstruction through Building Information Models (BIM) is a valuable methodology for documenting and analyzing existing buildings. Its pipeline starts with geometric acquisition. (e.g., via photogrammetry or laser scanning) for accurate point cloud collection. However, the acquired data are noisy and unstructured, and the creation of a semantically-meaningful BIM representation requires a huge computational effort, as well as expensive and time-consuming human annotations. In this paper, we propose a fully automated scan-to-BIM pipeline. The approach relies on: (i) our dataset (HePIC), acquired from two large buildings and annotated at a point-wise semantic level based on existent BIM models; (ii) a novel ad hoc deep network (BIM-Net++) for semantic segmentation, whose output is then processed to extract instance information necessary to recreate BIM objects; (iii) novel model pretraining and class re-weighting to eliminate the need for a large amount of labeled data and human intervention.
The Vision Transformer (ViT) leverages the Transformer's encoder to capture global information by dividing images into patches and achieves superior performance across various computer vision tasks. However, the self-attention mechanism of ViT captures the global context from the outset, overlooking the inherent relationships between neighboring pixels in images or videos. Transformers mainly focus on global information while ignoring the fine-grained local details. Consequently, ViT lacks inductive bias during image or video dataset training. In contrast, convolutional neural networks (CNNs), with their reliance on local filters, possess an inherent inductive bias, making them more efficient and quicker to converge than ViT with less data. In this paper, we present a lightweight Depth-Wise Convolution module as a shortcut in ViT models, bypassing entire Transformer blocks to ensure the models capture both local and global information with minimal overhead. Additionally, we introduce two architecture variants, allowing the Depth-Wise Convolution modules to be applied to multiple Transformer blocks for parameter savings, and incorporating independent parallel Depth-Wise Convolution modules with different kernels to enhance the acquisition of local information. The proposed approach significantly boosts the performance of ViT models on image classification, object detection, and instance segmentation by a large margin, especially on small datasets, as evaluated on CIFAR-10, CIFAR-100, Tiny-ImageNet and ImageNet for image classification, and COCO for object detection and instance segmentation. The source code can be accessed at https://github.com/ZTX-100/Efficient_ViT_with_DW.
Manually annotating nuclei from the gigapixel Hematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs) is a laborious and costly task, meaning automated algorithms for cell nuclei instance segmentation and classification could alleviate the workload of pathologists and clinical researchers and at the same time facilitate the automatic extraction of clinically interpretable features. But due to high intra- and inter-class variability of nuclei morphological and chromatic features, as well as H&E-stains susceptibility to artefacts, state-of-the-art algorithms cannot correctly detect and classify instances with the necessary performance. In this work, we hypothesise context and attention inductive biases in artificial neural networks (ANNs) could increase the generalization of algorithms for cell nuclei instance segmentation and classification. We conduct a thorough survey on context and attention methods for cell nuclei instance segmentation and classification from H&E-stained microscopy imaging, while providing a comprehensive discussion of the challenges being tackled with context and attention. Besides, we illustrate some limitations of current approaches and present ideas for future research. As a case study, we extend both a general instance segmentation and classification method (Mask-RCNN) and a tailored cell nuclei instance segmentation and classification model (HoVer-Net) with context- and attention-based mechanisms, and do a comparative analysis on a multi-centre colon nuclei identification and counting dataset. Although pathologists rely on context at multiple levels while paying attention to specific Regions of Interest (RoIs) when analysing and annotating WSIs, our findings suggest translating that domain knowledge into algorithm design is no trivial task, but to fully exploit these mechanisms, the scientific understanding of these methods should be addressed.
The precise segmentation and tracking of cells in microscopy image sequences play a pivotal role in biomedical research, facilitating the study of tissue, organ, and organism development. However, manual segmentation and tracking of cells is time-consuming and often require professional experiences. Besides, segmenting cells in the images with a low signal-to-noise ratio remains difficult. While deep learning (DL) has become a common method for cell segmentation, few DL- based methods address concurrent cell segmentation and tracking. In this paper, we propose a novel DL approach featuring graph-based tracking for cell segmentation and tracking in microscopy images. We combine Deeplabv3+ for semantic segmentation and ResNet50 for enhanced feature extraction, enabling comprehensive cell detection and instance segmentation. Post-processing, involving non-maxima suppression and outlier detection, refines predictions and produces final segmentation. The tracking method is based on the relative position of graph nodes to track segmented cells, encompassing cell division and apoptosis. We conduct our experiments on the induced pluripotent stem (iPS) cell datasets, and the results show that the segmentation and tracking performance of our method yields superior performance compared to the benchmark models. More specifically, our approach achieved DET values of 0.955 and 0.913, TRA values of 0.951 and 0.906, and SEG values of 0.690 and 0.665 on two iPS dataset videos, respectively. Additionally, the performance assessment encompasses four real microscopy datasets from the Cell Tracking Challenge (CTC). Our method greatly reduces the cost of manual labeling and labor-intensive costs.
The segmentation of cell nuclei in tissue images stained with the blood dye hematoxylin and eosin (H$\&$E) is essential for various clinical applications and analyses. Due to the complex characteristics of cellular morphology, a large receptive field is considered crucial for generating high-quality segmentation. However, previous methods face challenges in achieving a balance between the receptive field and computational burden. To address this issue, we propose LKCell, a high-accuracy and efficient cell segmentation method. Its core insight lies in unleashing the potential of large convolution kernels to achieve computationally efficient large receptive fields. Specifically, (1) We transfer pre-trained large convolution kernel models to the medical domain for the first time, demonstrating their effectiveness in cell segmentation. (2) We analyze the redundancy of previous methods and design a new segmentation decoder based on large convolution kernels. It achieves higher performance while significantly reducing the number of parameters. We evaluate our method on the most challenging benchmark and achieve state-of-the-art results (0.5080 mPQ) in cell nuclei instance segmentation with only 21.6% FLOPs compared with the previous leading method. Our source code and models are available at https://github.com/hustvl/LKCell.
Generative design (GD) methods aim to automatically generate a wide variety of designs that satisfy functional or aesthetic design requirements. However, research to date generally lacks considerations of manufacturability of the generated designs. To this end, we propose a novel GD approach by using deep neural networks to encode design for manufacturing (DFM) rules, thereby modifying part designs to make them manufacturable by a given manufacturing process. Specifically, a three-step approach is proposed: first, an instance segmentation method, Mask R-CNN, is used to decompose a part design into subregions. Second, a conditional generative adversarial neural network (cGAN), Pix2Pix, transforms unmanufacturable decomposed subregions into manufacturable subregions. The transformed subregions of designs are subsequently reintegrated into a unified manufacturable design. These three steps, Mask-RCNN, Pix2Pix, and reintegration, form the basis of the proposed Manufacturable conditional GAN (McGAN) framework. Experimental results show that McGAN can transform existing unmanufacturable designs to generate their corresponding manufacturable counterparts automatically that realize the specified manufacturing rules in an efficient and robust manner. The effectiveness of McGAN is demonstrated through two-dimensional design case studies of an injection molding process.
We present PartGLEE, a part-level foundation model for locating and identifying both objects and parts in images. Through a unified framework, PartGLEE accomplishes detection, segmentation, and grounding of instances at any granularity in the open world scenario. Specifically, we propose a Q-Former to construct the hierarchical relationship between objects and parts, parsing every object into corresponding semantic parts. By incorporating a large amount of object-level data, the hierarchical relationships can be extended, enabling PartGLEE to recognize a rich variety of parts. We conduct comprehensive studies to validate the effectiveness of our method, PartGLEE achieves the state-of-the-art performance across various part-level tasks and obtain competitive results on object-level tasks. The proposed PartGLEE significantly enhances hierarchical modeling capabilities and part-level perception over our previous GLEE model. Further analysis indicates that the hierarchical cognitive ability of PartGLEE is able to facilitate a detailed comprehension in images for mLLMs. The model and code will be released at https://provencestar.github.io/PartGLEE-Vision/ .
Accurately segmenting and individualizing cells in SEM images is a highly promising technique for elucidating tissue architecture in oncology. While current AI-based methods are effective, errors persist, necessitating time-consuming manual corrections, particularly in areas where the quality of cell contours in the image is poor and requires gap filling. This study presents a novel AI-driven approach for refining cell boundary delineation to improve instance-based cell segmentation in SEM images, also reducing the necessity for residual manual correction. A CNN COp-Net is introduced to address gaps in cell contours, effectively filling in regions with deficient or absent information. The network takes as input cell contour probability maps with potentially inadequate or missing information and outputs corrected cell contour delineations. The lack of training data was addressed by generating low integrity probability maps using a tailored PDE. We showcase the efficacy of our approach in augmenting cell boundary precision using both private SEM images from PDX hepatoblastoma tissues and publicly accessible images datasets. The proposed cell contour closing operator exhibits a notable improvement in tested datasets, achieving respectively close to 50% (private data) and 10% (public data) increase in the accurately-delineated cell proportion compared to state-of-the-art methods. Additionally, the need for manual corrections was significantly reduced, therefore facilitating the overall digitalization process. Our results demonstrate a notable enhancement in the accuracy of cell instance segmentation, particularly in highly challenging regions where image quality compromises the integrity of cell boundaries, necessitating gap filling. Therefore, our work should ultimately facilitate the study of tumour tissue bioarchitecture in onconanotomy field.