Click-based interactive segmentation aims to generate target masks via human clicking, which facilitates efficient pixel-level annotation and image editing. In such a task, target ambiguity remains a problem hindering the accuracy and efficiency of segmentation. That is, in scenes with rich context, one click may correspond to multiple potential targets, while most previous interactive segmentors only generate a single mask and fail to deal with target ambiguity. In this paper, we propose a novel interactive segmentation network named PiClick, to yield all potentially reasonable masks and suggest the most plausible one for the user. Specifically, PiClick utilizes a Transformer-based architecture to generate all potential target masks by mutually interactive mask queries. Moreover, a Target Reasoning module(TRM) is designed in PiClick to automatically suggest the user-desired mask from all candidates, relieving target ambiguity and extra-human efforts. Extensive experiments on 9 interactive segmentation datasets demonstrate PiClick performs favorably against previous state-of-the-arts considering the segmentation results. Moreover, we show that PiClick effectively reduces human efforts in annotating and picking the desired masks. To ease the usage and inspire future research, we release the source code of PiClick together with a plug-and-play annotation tool at https://github.com/cilinyan/PiClick.
Training segmentation models for medical images continues to be challenging due to the limited availability of data annotations. Segment Anything Model (SAM) is a foundation model that is intended to segment user-defined objects of interest in an interactive manner. While the performance on natural images is impressive, medical image domains pose their own set of challenges. Here, we perform an extensive evaluation of SAM's ability to segment medical images on a collection of 19 medical imaging datasets from various modalities and anatomies. We report the following findings: (1) SAM's performance based on single prompts highly varies depending on the dataset and the task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray. (2) Segmentation performance appears to be better for well-circumscribed objects with prompts with less ambiguity and poorer in various other scenarios such as the segmentation of brain tumors. (3) SAM performs notably better with box prompts than with point prompts. (4) SAM outperforms similar methods RITM, SimpleClick, and FocalClick in almost all single-point prompt settings. (5) When multiple-point prompts are provided iteratively, SAM's performance generally improves only slightly while other methods' performance improves to the level that surpasses SAM's point-based performance. We also provide several illustrations for SAM's performance on all tested datasets, iterative segmentation, and SAM's behavior given prompt ambiguity. We conclude that SAM shows impressive zero-shot segmentation performance for certain medical imaging datasets, but moderate to poor performance for others. SAM has the potential to make a significant impact in automated medical image segmentation in medical imaging, but appropriate care needs to be applied when using it.
Contrastive language-image pre-training (CLIP) is a powerful vision-language model that has shown great benefits for various tasks. However, we have identified some issues with its explainability, which undermine its credibility and limit the capacity for related tasks. Specifically, we find that CLIP tends to focus on background regions rather than foregrounds, with noisy activations at irrelevant positions on the visualization results. These phenomena conflict with conventional explainability methods based on the class attention map (CAM), where the raw model can highlight the local foreground regions using global supervision without alignment. To address these problems, we take a closer look at its architecture and features. Based on thorough analyses, we find the raw self-attentions link to inconsistent semantic regions, resulting in the opposite visualization. Besides, the noisy activations are owing to redundant features among categories. Building on these insights, we propose the CLIP Surgery for reliable CAM, a method that allows surgery-like modifications to the inference architecture and features, without further fine-tuning as classical CAM methods. This approach significantly improves the explainability of CLIP, surpassing existing methods by large margins. Besides, it enables multimodal visualization and extends the capacity of raw CLIP on open-vocabulary tasks without extra alignment. The code is available at https://github.com/xmed-lab/CLIP_Surgery.
Interactive image segmentation enables annotators to efficiently perform pixel-level annotation for segmentation tasks. However, the existing interactive segmentation pipeline suffers from inefficient computations of interactive models because of the following two issues. First, annotators' later click is based on models' feedback of annotators' former click. This serial interaction is unable to utilize model's parallelism capabilities. Second, in each interaction step, the model handles the invariant image along with the sparse variable clicks, resulting in a process that's highly repetitive and redundant. For efficient computations, we propose a method named InterFormer that follows a new pipeline to address these issues. InterFormer extracts and preprocesses the computationally time-consuming part i.e. image processing from the existing process. Specifically, InterFormer employs a large vision transformer (ViT) on high-performance devices to preprocess images in parallel, and then uses a lightweight module called interactive multi-head self attention (I-MSA) for interactive segmentation. Furthermore, the I-MSA module's deployment on low-power devices extends the practical application of interactive segmentation. The I-MSA module utilizes the preprocessed features to efficiently response to the annotator inputs in real-time. The experiments on several datasets demonstrate the effectiveness of InterFormer, which outperforms previous interactive segmentation models in terms of computational efficiency and segmentation quality, achieve real-time high-quality interactive segmentation on CPU-only devices. The code is available at https://github.com/YouHuang67/InterFormer.
Existing interactive segmentation methods leverage automatic segmentation and user interactions for label refinement, significantly reducing the annotation workload compared to manual annotation. However, these methods lack quick adaptability to ambiguous and noisy data, which is a challenge in CT volumes containing lung lesions from COVID-19 patients. In this work, we propose an adaptive multi-scale online likelihood network (MONet) that adaptively learns in a data-efficient online setting from both an initial automatic segmentation and user interactions providing corrections. We achieve adaptive learning by proposing an adaptive loss that extends the influence of user-provided interaction to neighboring regions with similar features. In addition, we propose a data-efficient probability-guided pruning method that discards uncertain and redundant labels in the initial segmentation to enable efficient online training and inference. Our proposed method was evaluated by an expert in a blinded comparative study on COVID-19 lung lesion annotation task in CT. Our approach achieved 5.86% higher Dice score with 24.67% less perceived NASA-TLX workload score than the state-of-the-art. Source code is available at: https://github.com/masadcv/MONet-MONAILabel
A robot operating in unstructured environments must be able to discriminate between different grasping styles depending on the prospective manipulation task. Having a system that allows learning from remote non-expert demonstrations can very feasibly extend the cognitive skills of a robot for task-oriented grasping. We propose a novel two-step framework towards this aim. The first step involves grasp area estimation by segmentation. We receive grasp area demonstrations for a new task via interactive segmentation, and learn from these few demonstrations to estimate the required grasp area on an unseen scene for the given task. The second step is autonomous grasp estimation in the segmented region. To train the segmentation network for few-shot learning, we built a grasp area segmentation (GAS) dataset with 10089 images grouped into 1121 segmentation tasks. We benefit from an efficient meta learning algorithm for training for few-shot adaptation. Experimental evaluation showed that our method successfully detects the correct grasp area on the respective objects in unseen test scenes and effectively allows remote teaching of new grasp strategies by non-experts.
The click-based interactive segmentation aims to extract the object of interest from an image with the guidance of user clicks. Recent work has achieved great overall performance by employing feedback from the output. However, in most state-of-the-art approaches, 1) the inference stage involves inflexible heuristic rules and requires a separate refinement model, and 2) the number of user clicks and model performance cannot be balanced. To address the challenges, we propose a click-based and mask-guided interactive image segmentation framework containing three novel components: Cascade-Forward Refinement (CFR), Iterative Click Loss (ICL), and SUEM image augmentation. The CFR offers a unified inference framework to generate segmentation results in a coarse-to-fine manner. The proposed ICL allows model training to improve segmentation and reduce user interactions simultaneously. The proposed SUEM augmentation is a comprehensive way to create large and diverse training sets for interactive image segmentation. Extensive experiments demonstrate the state-of-the-art performance of the proposed approach on five public datasets. Remarkably, our model reduces by 33.2\%, and 15.5\% the number of clicks required to surpass an IoU of 0.95 in the previous state-of-the-art approach on the Berkeley and DAVIS sets, respectively.
Click-based interactive segmentation (IS) aims to extract the target objects under user interaction. For this task, most of the current deep learning (DL)-based methods mainly follow the general pipelines of semantic segmentation. Albeit achieving promising performance, they do not fully and explicitly utilize and propagate the click information, inevitably leading to unsatisfactory segmentation results, even at clicked points. Against this issue, in this paper, we propose to formulate the IS task as a Gaussian process (GP)-based pixel-wise binary classification model on each image. To solve this model, we utilize amortized variational inference to approximate the intractable GP posterior in a data-driven manner and then decouple the approximated GP posterior into double space forms for efficient sampling with linear complexity. Then, we correspondingly construct a GP classification framework, named GPCIS, which is integrated with the deep kernel learning mechanism for more flexibility. The main specificities of the proposed GPCIS lie in: 1) Under the explicit guidance of the derived GP posterior, the information contained in clicks can be finely propagated to the entire image and then boost the segmentation; 2) The accuracy of predictions at clicks has good theoretical support. These merits of GPCIS as well as its good generality and high efficiency are substantiated by comprehensive experiments on several benchmarks, as compared with representative methods both quantitatively and qualitatively.
Recently, deep learning enabled the accurate segmentation of various diseases in medical imaging. These performances, however, typically demand large amounts of manual voxel annotations. This tedious process for volumetric data becomes more complex when not all required information is available in a single imaging domain as is the case for PET/CT data. We propose a multimodal interactive segmentation framework that mitigates these issues by combining anatomical and physiological cues from PET/CT data. Our framework utilizes the geodesic distance transform to represent the user annotations and we implement a novel ellipsoid-based user simulation scheme during training. We further propose two annotation interfaces and conduct a user study to estimate their usability. We evaluated our model on the in-domain validation dataset and an unseen PET/CT dataset. We make our code publicly available: https://github.com/verena-hallitschke/pet-ct-annotate.
Click-based interactive image segmentation aims at extracting objects with a limited user clicking. A hierarchical backbone is the de-facto architecture for current methods. Recently, the plain, non-hierarchical Vision Transformer (ViT) has emerged as a competitive backbone for dense prediction tasks. This design allows the original ViT to be a foundation model that can be finetuned for downstream tasks without redesigning a hierarchical backbone for pretraining. Although this design is simple and has been proven effective, it has not yet been explored for interactive image segmentation. To fill this gap, we propose SimpleClick, the first interactive segmentation method that leverages a plain backbone. Based on the plain backbone, we introduce a symmetric patch embedding layer that encodes clicks into the backbone with minor modifications to the backbone itself. With the plain backbone pretrained as a masked autoencoder (MAE), SimpleClick achieves state-of-the-art performance. Remarkably, our method achieves 4.15 NoC@90 on SBD, improving 21.8% over the previous best result. Extensive evaluation on medical images demonstrates the generalizability of our method. We further develop an extremely tiny ViT backbone for SimpleClick and provide a detailed computational analysis, highlighting its suitability as a practical annotation tool.
In recent years, the rapid development of deep learning has brought great advancements to image and video segmentation methods based on neural networks. However, to unleash the full potential of such models, large numbers of high-quality annotated images are necessary for model training. Currently, many widely used open-source image segmentation software relies heavily on manual annotation which is tedious and time-consuming. In this work, we introduce EISeg, an Efficient Interactive SEGmentation annotation tool that can drastically improve image segmentation annotation efficiency, generating highly accurate segmentation masks with only a few clicks. We also provide various domain-specific models for remote sensing, medical imaging, industrial quality inspections, human segmentation, and temporal aware models for video segmentation. The source code for our algorithm and user interface are available at: https://github.com/PaddlePaddle/PaddleSeg.
The FastGeodis package provides an efficient implementation for computing Geodesic and Euclidean distance transforms (or a mixture of both), targeting efficient utilisation of CPU and GPU hardware. In particular, it implements the paralellisable raster scan method from Criminisi et al. (2009), where elements in a row (2D) or plane (3D) can be computed with parallel threads. This package is able to handle 2D as well as 3D data, where it achieves up to a 20x speedup on a CPU and up to a 74x speedup on a GPU as compared to an existing open-source library (Wang, 2020) that uses a non-parallelisable single-thread CPU implementation. The performance speedups reported here were evaluated using 3D volume data on an Nvidia GeForce Titan X (12 GB) with a 6-Core Intel Xeon E5-1650 CPU. Further in-depth comparison of performance improvements are discussed in the FastGeodis documentation: https://fastgeodis.readthedocs.io
We introduce an interactive image segmentation and visualization framework for identifying, inspecting, and editing tiny objects (just a few pixels wide) in large multi-megapixel high-dynamic-range (HDR) images. Detecting cosmic rays (CRs) in astronomical observations is a cumbersome workflow that requires multiple tools, so we developed an interactive toolkit that unifies model inference, HDR image visualization, segmentation mask inspection and editing into a single graphical user interface. The feature set, initially designed for astronomical data, makes this work a useful research-supporting tool for human-in-the-loop tiny-object segmentation in scientific areas like biomedicine, materials science, remote sensing, etc., as well as computer vision. Our interface features mouse-controlled, synchronized, dual-window visualization of the image and the segmentation mask, a critical feature for locating tiny objects in multi-megapixel images. The browser-based tool can be readily hosted on the web to provide multi-user access and GPU acceleration for any device. The toolkit can also be used as a high-precision annotation tool, or adapted as the frontend for an interactive machine learning framework. Our open-source dataset, CR detection model, and visualization toolkit are available at https://github.com/cy-xu/cosmic-conn.
Interactive segmentation allows users to extract target masks by making positive/negative clicks. Although explored by many previous works, there is still a gap between academic approaches and industrial needs: first, existing models are not efficient enough to work on low power devices; second, they perform poorly when used to refine preexisting masks as they could not avoid destroying the correct part. FocalClick solves both issues at once by predicting and updating the mask in localized areas. For higher efficiency, we decompose the slow prediction on the entire image into two fast inferences on small crops: a coarse segmentation on the Target Crop, and a local refinement on the Focus Crop. To make the model work with preexisting masks, we formulate a sub-task termed Interactive Mask Correction, and propose Progressive Merge as the solution. Progressive Merge exploits morphological information to decide where to preserve and where to update, enabling users to refine any preexisting mask effectively. FocalClick achieves competitive results against SOTA methods with significantly smaller FLOPs. It also shows significant superiority when making corrections on preexisting masks. Code and data will be released at github.com/XavierCHEN34/ClickSEG
We aim to tackle the problem of point-based interactive segmentation, in which the key challenge is to propagate the user-provided annotations to unlabeled regions efficiently. Existing methods tackle this challenge by utilizing computationally expensive fully connected graphs or transformer architectures that sacrifice important fine-grained information required for accurate segmentation. To overcome these limitations, we propose a cascade sparse feature propagation network that learns a click-augmented feature representation for propagating user-provided information to unlabeled regions. The sparse design of our network enables efficient information propagation on high-resolution features, resulting in more detailed object segmentation. We validate the effectiveness of our method through comprehensive experiments on various benchmarks, and the results demonstrate the superior performance of our approach. Code is available at \href{https://github.com/kleinzcy/CSFPN}{https://github.com/kleinzcy/CSFPN}.
Automatic segmentation of lung lesions associated with COVID-19 in CT images requires large amount of annotated volumes. Annotations mandate expert knowledge and are time-intensive to obtain through fully manual segmentation methods. Additionally, lung lesions have large inter-patient variations, with some pathologies having similar visual appearance as healthy lung tissues. This poses a challenge when applying existing semi-automatic interactive segmentation techniques for data labelling. To address these challenges, we propose an efficient convolutional neural networks (CNNs) that can be learned online while the annotator provides scribble-based interaction. To accelerate learning from only the samples labelled through user-interactions, a patch-based approach is used for training the network. Moreover, we use weighted cross-entropy loss to address the class imbalance that may result from user-interactions. During online inference, the learned network is applied to the whole input volume using a fully convolutional approach. We compare our proposed method with state-of-the-art using synthetic scribbles and show that it outperforms existing methods on the task of annotating lung lesions associated with COVID-19, achieving 16% higher Dice score while reducing execution time by 3$\times$ and requiring 9000 lesser scribbles-based labelled voxels. Due to the online learning aspect, our approach adapts quickly to user input, resulting in high quality segmentation labels. Source code for ECONet is available at: https://github.com/masadcv/ECONet-MONAILabel.
We propose iSegFormer, a memory-efficient transformer that combines a Swin transformer with a lightweight multilayer perceptron (MLP) decoder. With the efficient Swin transformer blocks for hierarchical self-attention and the simple MLP decoder for aggregating both local and global attention, iSegFormer learns powerful representations while achieving high computational efficiencies. Specifically, we apply iSegFormer to interactive 3D medical image segmentation.
High-quality training data play a key role in image segmentation tasks. Usually, pixel-level annotations are expensive, laborious and time-consuming for the large volume of training data. To reduce labelling cost and improve segmentation quality, interactive segmentation methods have been proposed, which provide the result with just a few clicks. However, their performance does not meet the requirements of practical segmentation tasks in terms of speed and accuracy. In this work, we propose EdgeFlow, a novel architecture that fully utilizes interactive information of user clicks with edge-guided flow. Our method achieves state-of-the-art performance without any post-processing or iterative optimization scheme. Comprehensive experiments on benchmarks also demonstrate the superiority of our method. In addition, with the proposed method, we develop an efficient interactive segmentation tool for practical data annotation tasks. The source code and tool is avaliable at https://github.com/PaddlePaddle/PaddleSeg.
We provide a probabilistic interpretation of attention and show that the standard dot-product attention in transformers is a special case of Maximum A Posteriori (MAP) inference. The proposed approach suggests the use of Expectation Maximization algorithms for online adaptation of key and value model parameters. This approach is useful for cases in which external agents, e.g., annotators, provide inference-time information about the correct values of some tokens, e.g, the semantic category of some pixels, and we need for this new information to propagate to other tokens in a principled manner. We illustrate the approach on an interactive semantic segmentation task in which annotators and models collaborate online to improve annotation efficiency. Using standard benchmarks, we observe that key adaptation boosts model performance ($\sim10\%$ mIoU) in the low feedback regime and value propagation improves model responsiveness in the high feedback regime. A PyTorch layer implementation of our probabilistic attention model will be made publicly available here: https://github.com/apple/ml-probabilistic-attention.
Despite recent progress of automatic medical image segmentation techniques, fully automatic results usually fail to meet the clinical use and typically require further refinement. In this work, we propose a quality-aware memory network for interactive segmentation of 3D medical images. Provided by user guidance on an arbitrary slice, an interaction network is firstly employed to obtain an initial 2D segmentation. The quality-aware memory network subsequently propagates the initial segmentation estimation bidirectionally over the entire volume. Subsequent refinement based on additional user guidance on other slices can be incorporated in the same manner. To further facilitate interactive segmentation, a quality assessment module is introduced to suggest the next slice to segment based on the current segmentation quality of each slice. The proposed network has two appealing characteristics: 1) The memory-augmented network offers the ability to quickly encode past segmentation information, which will be retrieved for the segmentation of other slices; 2) The quality assessment module enables the model to directly estimate the qualities of segmentation predictions, which allows an active learning paradigm where users preferentially label the lowest-quality slice for multi-round refinement. The proposed network leads to a robust interactive segmentation engine, which can generalize well to various types of user annotations (e.g., scribbles, boxes). Experimental results on various medical datasets demonstrate the superiority of our approach in comparison with existing techniques.