Annotation Time Research Articles

Standard observation plane annotation for diagnosis of ossicular chain in the temporal bone CT images.

Temporal bone CT is an essential technique for diagnosing ossicular chain trauma, and the location of standard observation planes (SOP) is the foundation of imaging diagnosis. The ossicular chain is small in volume, and there are about 11 standard observation planes for ossicular chain diagnosis, so it is a professional and time-consuming task to label SOPs accurately. An automatic annotation method of SOP is proposed. Firstly, an SOP-Graph model is introduced to represent the spatial relative position of different SOPs and the radiologists' SOP searching experience. Secondly, based on the precise segmentation of auditory ossicles, an SOP annotation algorithm was proposed to implement the parameter estimation of the SOP Graph. Finally, the evaluation of ossicular chain SOP localization was conducted, which converts the intensive SOP labeling task to automatic labeling and subjective verification. In the experiments, 610 CT images of temporal bone were automatically annotated, and the average success rate of annotation was 65.8% after being verified by a radiologist. By converting the manual annotation to automatic annotation and subjective verification, the annotation time of one case was reduced from 12 min to about 2 min. A data set that included 4414 SOP annotated slices was established.

Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data

BackgroundImaging-based spatial transcriptomics technologies allow us to explore spatial gene expression profiles at the cellular level. Cell type annotation of imaging-based spatial data is challenging due to the small gene panel, but it is a crucial step for downstream analyses. Many good reference-based cell type annotation tools have been developed for single-cell RNA sequencing and sequencing-based spatial transcriptomics data. However, the performance of the reference-based cell type annotation tools on imaging-based spatial transcriptomics data has not been well studied yet.ResultsWe compared performance of five reference-based methods (SingleR, Azimuth, RCTD, scPred and scmapCell) with the marker-gene-based manual annotation method on an imaging-based Xenium data of human breast cancer. A practical workflow has been demonstrated for preparing a high-quality single-cell RNA reference, evaluating the accuracy, and estimating the running time for reference-based cell type annotation tools.ConclusionsSingleR was the best performing reference-based cell type annotation tool for the Xenium platform, being fast, accurate and easy to use, with results closely matching those of manual annotation.

JointNet4BCD: A Semi-Supervised Joint Learning Neural Network with Decision Fusion for Building Change Detection

Remote sensing image building change detection aims to identify building changes that occur in remote sensing images of the same areas acquired at different times. In recent years, the development of deep learning has led to significant advancements in building change detection methods. However, these fully supervised methods require a large number of bi-temporal remote sensing images with pixel-wise change detection labels to train the model, which incurs substantial time and manpower for annotation. To address this issue, this study proposes a novel single-temporal semi-supervised joint learning framework for building change detection, called JointNet4BCD. Firstly, to reduce annotation costs, we design a semi-supervised learning manner to train our model using a small number of building extraction labels instead of a large amount of building change detection labels. Furthermore, to improve the semantic understanding capability of the model, we propose a joint learning approach for building extraction and change detection tasks. Lastly, a decision fusion block is designed to fuse the building extraction results into the building change detection results to further improve the accuracy of building change detection. Experimental results on the two widely used datasets demonstrate that the proposed JointNet4BCD achieves excellent building change detection performance while reducing the need for labels from thousands to dozens. Using only ten labeled images, JointNet4BCD achieved F1-Scores of 83.93% and 83.45% on the LEVIR2000 and WHU datasets, respectively.

Integrating YOLOv7 with FixMatch for Enhancing Vehicle Detection Performance in Mixed Traffic Environments

A major challenge in the development of object detection technology is the significant reliance on large labeled datasets, which requires substantial time and memory for manual annotation—especially in complex, mixed traffic environments with varied vehicle types, congestion levels, and unpredictable motion patterns. This study addresses this issue by integrating the semi-supervised learning technique, FixMatch, into the YOLOv7 object detection model, utilizing 4000 transportation-related datasets. The FixMatch technique enables the model to detect unlabeled objects effectively through strong and weak augmentation methods. In this study, the detected objects in the mixed traffic environment include public transportation, pedicabs, cars, motorcycles, and trucks. This study achieved an impressive 97.5% detection accuracy by leveraging unlabeled data, demonstrating the model's efficiency and effectiveness in identifying vehicles under diverse traffic conditions. Consequently, integrating the FixMatch method into YOLOv7 provides a practical and efficient solution for object detection in situations where collecting labeled data is challenging, such as in dynamic and highly variable traffic environments.

Shape-Aware Adversarial Learning for Scribble-Supervised Medical Image Segmentation with a MaskMix Siamese Network: A Case Study of Cardiac MRI Segmentation.

The transition in medical image segmentation from fine-grained to coarse-grained annotation methods, notably scribble annotation, offers a practical and efficient preparation for deep learning applications. However, these methods often compromise segmentation precision and result in irregular contours. This study targets the enhancement of scribble-supervised segmentation to match the accuracy of fine-grained annotation. Capitalizing on the consistency of target shapes across unpaired datasets, this study introduces a shape-aware scribble-supervised learning framework (MaskMixAdv) addressing two critical tasks: (1) Pseudo label generation, where a mixup-based masking strategy enables image-level and feature-level data augmentation to enrich coarse-grained scribbles annotations. A dual-branch siamese network is proposed to generate fine-grained pseudo labels. (2) Pseudo label optimization, where a CNN-based discriminator is proposed to refine pseudo label contours by distinguishing them from external unpaired masks during model fine-tuning. MaskMixAdv works under constrained annotation conditions as a label-efficient learning approach for medical image segmentation. A case study on public cardiac MRI datasets demonstrated that the proposed MaskMixAdv outperformed the state-of-the-art methods and narrowed the performance gap between scribble-supervised and mask-supervised segmentation. This innovation cuts annotation time by at least 95%, with only a minor impact on Dice performance, specifically a 2.6% reduction. The experimental outcomes indicate that employing efficient and cost-effective scribble annotation can achieve high segmentation accuracy, significantly reducing the typical requirement for fine-grained annotations.

Rapid detection of mouse spermatogenic defects by testicular cellular composition analysis via enhanced deep learning model.

Histological analysis of the testicular sections is paramount in infertility research but tedious and often requires months of training and practice. Establish an expeditious histopathological analysis of mutant mice testicular sections stained with commonly available hematoxylin and eosin (H&E) via enhanced deep learning model MATERIALS AND METHODS: Automated segmentation and cellular composition analysis on the testes of six mouse reproductive mutants of key reproductive gene family, DAZ and PUMILIO gene family via H&E-stained mouse testicular sections. We improved the deep learning model with human interaction to achieve better pixel accuracy and reduced annotation time for histologists; revealed distinctive cell composition features consistent with previously published phenotypes for four mutants and novel spermatogenic defects in two newly generated mutants; established a fast spermatogenic defect detection protocol for quantitative and qualitative assessment of testicular defects within 2.5-3h, requiring as few as 8 H&E-stained testis sections; uncovered novel defects in AcDKO and a meiotic arrest defect in HDBKO, supporting the synergistic interaction of Sertoli Pum1 and Pum2 as well as redundant meiotic function of Dazl and Boule. Our testicular compositional analysis not only could reveal spermatogenic defects from staged seminiferous tubules but also from unstaged seminiferous tubule sections. Our SCSD-Net model offers a rapid protocol for detecting reproductive defects from H&E-stained testicular sections in as few as 3h, providing both quantitative and qualitative assessments of spermatogenic defects. Our analysis uncovered evidence supporting the synergistic interaction of Sertoli PUM1 and PUM2 in maintaining average testis size, and redundant roles of DAZ family proteins DAZL and BOULE in meiosis.

Enhancing Multi-Object Detection in Ultrasound Images Through Semi-Supervised Learning, Focal Loss and Relation of Frame

To identify musculoskeletal anatomical structures in real time by using deep learning techniques. An automated annotation system based on deep learning neural networks was designed to aid in the real-time identification of anatomical structures. Additionally, novel algorithms aimed at diminishing model training duration while enhancing accuracy were introduced. In this study, we proposed a semi-supervised learning (SSL) approach that substantially reduced annotation time. We also adopted the focal loss (FL) method to enhance the accuracy of challenging structures. Additionally, during the inference stage, we harnessed the temporal continuity of video frames, which involved leveraging information from preceding frames to facilitate recognition of structures in the current image. Training the model through a combination of SSL and FL yielded superior performance compared with supervised learning, while also substantially mitigating any expense linked to annotations. During inference, the incorporation of frame continuity helped to avoid discontinuity and bolster accuracy. Forearm tissue detection was demonstrated by properly configuring the SSL approach, including FL and the filtering threshold. Comparable performance with supervised learning was achieved while only using 30% of the training data. The real-time experimental results also demonstrated that implementing relation of frame reduced the number of missing frames during inference and successfully increased the confidence scores of detected objects. This proposed system has the potential to aid medical professionals in efficiently and effectively diagnosing musculoskeletal disorders, ultimately leading to enhanced patient outcomes.

Accelerating Clinical Text Annotation in Underrepresented Languages: A Case Study on Text De-Identification.

Clinical notes contain valuable information for research and monitoring quality of care. Named Entity Recognition (NER) is the process for identifying relevant pieces of information such as diagnoses, treatments, side effects, etc., and bring them to a more structured form. Although recent advancements in deep learning have facilitated automated recognition, particularly in English, NER can still be challenging due to limited specialized training data. This exacerbated in hospital settings where annotations are costly to obtain without appropriate incentives and often dependent on local specificities. In this work, we study whether this annotation process can be effectively accelerated by combining two practical strategies. First, we convert usually passive annotation tasks into a proactive contest to motivate human annotators in performing a task often considered tedious and time-consuming. Second, we provide pre-annotations for the participants to evaluate how recall and precision of the pre-annotations can boost or deteriorate annotation performance. We applied both strategies to a text de-identification task on French clinical notes and discharge summaries at a large Swiss university hospital. Our results show that proactive contest and average quality pre-annotations can significantly speed up annotation time and increase annotation quality, enabling us to develop a text de-identification model for French clinical notes with high performance (F1 score 0.94).

CLIP-FSSC: A transferable visual model for fish and shrimp species classification based on natural language supervision

CLIP-FSSC: A transferable visual model for fish and shrimp species classification based on natural language supervision

Probing perfection: The relentless art of meddling for pulmonary airway segmentation from HRCT via a human-AI collaboration based active learning method

In the realm of pulmonary tracheal segmentation, the scarcity of annotated data stands as a prevalent pain point in most medical segmentation endeavors. Concurrently, most Deep Learning (DL) methodologies employed in this domain invariably grapple with other dual challenges: the inherent opacity of 'black box' models and the ongoing pursuit of performance enhancement. In response to these intertwined challenges, the core concept of our Human-Computer Interaction (HCI) based learning models (RS_UNet, LC_UNet, UUNet and WD_UNet) hinge on the versatile combination of diverse query strategies and an array of deep learning models. We train four HCI models based on the initial training dataset and sequentially repeat the following steps 1-4: (1) Query Strategy: Our proposed HCI models selects those samples which contribute the most additional representative information when labeled in each iteration of the query strategy (showing the names and sequence numbers of the samples to be annotated). Additionally, in this phase, the model selects the unlabeled samples with the greatest predictive disparity by calculating the Wasserstein Distance, Least Confidence, Entropy Sampling, and Random Sampling. (2) Central line correction: The selected samples in previous stage are then used for domain expert correction of the system-generated tracheal central lines in each training round. (3) Update training dataset: When domain experts are involved in each epoch of the DL model's training iterations, they update the training dataset with greater precision after each epoch, thereby enhancing the trustworthiness of the 'black box' DL model and improving the performance of models. (4) Model training: Proposed HCI model is trained using the updated training dataset and an enhanced version of existing UNet. Experimental results validate the effectiveness of this Human-Computer Interaction-based approaches, demonstrating that our proposed WD-UNet, LC-UNet, UUNet, RS-UNet achieve comparable or even superior performance than the state-of-the-art DL models, such as WD-UNet with only 15%-35% of the training data, leading to substantial reductions (65%-85% reduction of annotation effort) in physician annotation time.

Is Boundary Annotation Necessary? Evaluating Boundary-Free Approaches to Improve Clinical Named Entity Annotation Efficiency: Case Study.

Named entity recognition (NER) is a fundamental task in natural language processing. However, it is typically preceded by named entity annotation, which poses several challenges, especially in the clinical domain. For instance, determining entity boundaries is one of the most common sources of disagreements between annotators due to questions such as whether modifiers or peripheral words should be annotated. If unresolved, these can induce inconsistency in the produced corpora, yet, on the other hand, strict guidelines or adjudication sessions can further prolong an already slow and convoluted process. The aim of this study is to address these challenges by evaluating 2 novel annotation methodologies, lenient span and point annotation, aiming to mitigate the difficulty of precisely determining entity boundaries. We evaluate their effects through an annotation case study on a Japanese medical case report data set. We compare annotation time, annotator agreement, and the quality of the produced labeling and assess the impact on the performance of an NER system trained on the annotated corpus. We saw significant improvements in the labeling process efficiency, with up to a 25% reduction in overall annotation time and even a 10% improvement in annotator agreement compared to the traditional boundary-strict approach. However, even the best-achieved NER model presented some drop in performance compared to the traditional annotation methodology. Our findings demonstrate a balance between annotation speed and model performance. Although disregarding boundary information affects model performance to some extent, this is counterbalanced by significant reductions in the annotator's workload and notable improvements in the speed of the annotation process. These benefits may prove valuable in various applications, offering an attractive compromise for developers and researchers.

Highly precise community science annotations of video camera‐trapped fauna in challenging environments

AbstractAs camera trapping grows in popularity and application, some analytical limitations persist including processing time and accuracy of data annotation. Typically images are recorded by camera traps although videos are becoming increasingly collected even though they require much more time for annotation. To overcome limitations with image annotation, camera trap studies are increasingly linked to community science (CS) platforms. Here, we extend previous work on CS image annotations to camera trap videos from a challenging environment; a dense tropical forest with low visibility and high occlusion due to thick canopy cover and bushy undergrowth at the camera level. Using the CS platform Chimp&See, established for classification of 599 956 video clips from tropical Africa, we assess annotation precision and accuracy by comparing classification of 13 531 1‐min video clips by a professional ecologist (PE) with output from 1744 registered, as well as unregistered, Chimp&See community scientists. We considered 29 classification categories, including 17 species and 12 higher‐level categories, in which phenotypically similar species were grouped. Overall, annotation precision was 95.4%, which increased to 98.2% when aggregating similar species groups together. Our findings demonstrate the competence of community scientists working with camera trap videos from even challenging environments and hold great promise for future studies on animal behaviour, species interaction dynamics and population monitoring.

WSPolyp-SAM: Weakly Supervised and Self-Guided Fine-Tuning of SAM for Colonoscopy Polyp Segmentation

Ensuring precise segmentation of colorectal polyps holds critical importance in the early diagnosis and treatment of colorectal cancer. Nevertheless, existing deep learning-based segmentation methods are fully supervised, requiring extensive, precise, manual pixel-level annotation data, which leads to high annotation costs. Additionally, it remains challenging to train large-scale segmentation models when confronted with limited colonoscopy data. To address these issues, we introduce the general segmentation foundation model—the Segment Anything Model (SAM)—into the field of medical image segmentation. Fine-tuning the foundation model is an effective approach to tackle sample scarcity. However, current SAM fine-tuning techniques still rely on precise annotations. To overcome this limitation, we propose WSPolyp-SAM, a novel weakly supervised approach for colonoscopy polyp segmentation. WSPolyp-SAM utilizes weak annotations to guide SAM in generating segmentation masks, which are then treated as pseudo-labels to guide the fine-tuning of SAM, thereby reducing the dependence on precise annotation data. To improve the reliability and accuracy of pseudo-labels, we have designed a series of enhancement strategies to improve the quality of pseudo-labels and mitigate the negative impact of low-quality pseudo-labels. Experimental results on five medical image datasets demonstrate that WSPolyp-SAM outperforms current fully supervised mainstream polyp segmentation networks on the Kvasir-SEG, ColonDB, CVC-300, and ETIS datasets. Furthermore, by using different amounts of training data in weakly supervised and fully supervised experiments, it is found that weakly supervised fine-tuning can save 70% to 73% of annotation time costs compared to fully supervised fine-tuning. This study provides a new perspective on the combination of weakly supervised learning and SAM models, significantly reducing annotation time and offering insights for further development in the field of colonoscopy polyp segmentation.

Deep learning-based liver cyst segmentation in MRI for autosomal dominant polycystic kidney disease

Abstract Background Autosomal dominant polycystic kidney disease (ADPKD) can lead to polycystic liver disease (PLD), characterized by liver cysts. Although majority of the patients are asymptomatic, massively enlarged liver secondary to PLD can cause discomfort, and compression on adjacent structures requiring cyst aspiration/fenestration, partial liver resection, or liver transplantation. Monitoring PLD by measuring liver volume fails to track the early stages when liver cyst volume is too small to affect liver volume. Purpose To improve PLD assessment in the early stages by automating detection and segmentation of liver cysts using deep learning (DL) models. Materials and Methods A self-configured UNet-based platform (nnU-Net) was trained with 40 ADPKD subjects with liver cysts annotated by a radiologist. Internal (n = 7), External (n = 10), and test-retest reproducibility (n = 17) validations included macro- and micro-level performance metrics: patient-level Dice scores (PDice), along with voxel-level true positive rates (VTPR), as well as analysis of time saved in a model-assisted scenario. Additionally, we assessed human-level reliability in liver cyst segmentation and evaluated the model’s test-retest reproducibility. We further compared liver volume vs cyst volume for tracking disease in a subject with 16+ years follow-up. Results The model achieved an 82% ± 11% PDice and a 75% ± 15% VTPR on the internal test sets (n = 7 patients), and 80% ± 12% Dice score and a 91% ± 7% VTPR on the external test sets (n = 10 patients). It excelled particularly in detecting small liver cysts, a challenging task for manual annotation. This efficiency translated to a median of 91% (IQR: 14%) reduction in annotation time compared to manual labeling. Test-retest assessment demonstrated excellent reproducibility, with coefficients of variation of 94% for liver cyst fraction and 92% for cyst count. Conclusion DL automation of liver cyst segmentations demonstrates potential to improve tracking of liver cyst volume in polycystic liver disease.

MONAI Label: A framework for AI-assisted interactive labeling of 3D medical images

The lack of annotated datasets is a major bottleneck for training new task-specific supervised machine learning models, considering that manual annotation is extremely expensive and time-consuming. To address this problem, we present MONAI Label, a free and open-source framework that facilitates the development of applications based on artificial intelligence (AI) models that aim at reducing the time required to annotate radiology datasets. Through MONAI Label, researchers can develop AI annotation applications focusing on their domain of expertise. It allows researchers to readily deploy their apps as services, which can be made available to clinicians via their preferred user interface. Currently, MONAI Label readily supports locally installed (3D Slicer) and web-based (OHIF) frontends and offers two active learning strategies to facilitate and speed up the training of segmentation algorithms. MONAI Label allows researchers to make incremental improvements to their AI-based annotation application by making them available to other researchers and clinicians alike. Additionally, MONAI Label provides sample AI-based interactive and non-interactive labeling applications, that can be used directly off the shelf, as plug-and-play to any given dataset. Significant reduced annotation times using the interactive model can be observed on two public datasets.

FLAIR MRI sequence synthesis using squeeze attention generative model for reliable brain tumor segmentation

FLAIR MRI sequence synthesis using squeeze attention generative model for reliable brain tumor segmentation

RegWSI: Whole slide image registration using combined deep feature- and intensity-based methods: Winner of the ACROBAT 2023 challenge

The automatic registration of differently stained whole slide images (WSIs) is crucial for improving diagnosis and prognosis by fusing complementary information emerging from different visible structures. It is also useful to quickly transfer annotations between consecutive or restained slides, thus significantly reducing the annotation time and associated costs. Nevertheless, the slide preparation is different for each stain and the tissue undergoes complex and large deformations. Therefore, a robust, efficient, and accurate registration method is highly desired by the scientific community and hospitals specializing in digital pathology. We propose a two-step hybrid method consisting of (i) deep learning- and feature-based initial alignment algorithm, and (ii) intensity-based nonrigid registration using the instance optimization. The proposed method does not require any fine-tuning to a particular dataset and can be used directly for any desired tissue type and stain. The registration time is low, allowing one to perform efficient registration even for large datasets. The method was proposed for the ACROBAT 2023 challenge organized during the MICCAI 2023 conference and scored 1st place. The method is released as open-source software. The proposed method is evaluated using three open datasets: (i) Automatic Nonrigid Histological Image Registration Dataset (ANHIR), (ii) Automatic Registration of Breast Cancer Tissue Dataset (ACROBAT), and (iii) Hybrid Restained and Consecutive Histological Serial Sections Dataset (HyReCo). The target registration error (TRE) is used as the evaluation metric. We compare the proposed algorithm to other state-of-the-art solutions, showing considerable improvement. Additionally, we perform several ablation studies concerning the resolution used for registration and the initial alignment robustness and stability. The method achieves the most accurate results for the ACROBAT dataset, the cell-level registration accuracy for the restained slides from the HyReCo dataset, and is among the best methods evaluated on the ANHIR dataset. The article presents an automatic and robust registration method that outperforms other state-of-the-art solutions. The method does not require any fine-tuning to a particular dataset and can be used out-of-the-box for numerous types of microscopic images. The method is incorporated into the DeeperHistReg framework, allowing others to directly use it to register, transform, and save the WSIs at any desired pyramid level (resolution up to 220k x 220k). We provide free access to the software. The results are fully and easily reproducible. The proposed method is a significant contribution to improving the WSI registration quality, thus advancing the field of digital pathology.

Using spatiotemporal information in weather radar data to detect and track communal roosts

AbstractThe exodus of flying animals from their roosting locations is often visible as expanding ring‐shaped patterns in weather radar data. The NEXRAD network, for example, archives more than 25 years of data across 143 contiguous US radar stations, providing opportunities to study roosting locations and times and the ecosystems of birds and bats. However, access to this information is limited by the cost of manually annotating millions of radar scans. We develop and deploy an AI‐assisted system to annotate roosts in radar data. We build datasets with roost annotations to support the training and evaluation of automated detection models. Roosts are detected, tracked, and incorporated into our developed web‐based interface for human screening to produce research‐grade annotations. We deploy the system to collect swallow and martin roost information from 12 radar stations around the Great Lakes spanning 21 years. After verifying the practical value of the system, we propose to improve the detector by incorporating both spatial and temporal channels from volumetric radar scans. The deployment on Great Lakes radar scans allows accelerated annotation of 15 628 roost signatures in 612 786 radar scans with 183.6 human screening hours, or 1.08 s per radar scan. We estimate that the deployed system reduces human annotation time by ~7×. The temporal detector model improves the average precision at intersection‐over‐union threshold 0.5 (APIoU = .50) by 8% over the previous model (48%→56%), further reducing human screening time by 2.3× in its pilot deployment. These data contain critical information about phenology and population trends of swallows and martins, aerial insectivore species experiencing acute declines, and have enabled novel research. We present error analyses, lay the groundwork for continent‐scale historical investigation about these species, and provide a starting point for automating the detection of other family‐specific phenomena in radar data, such as bat roosts and mayfly hatches.

On-the-fly point annotation for fast medical video labeling.

In medical research, deep learning models rely on high-quality annotated data, a process often laborious and time-consuming. This is particularly true for detection tasks where bounding box annotations are required. The need to adjust two corners makes the process inherently frame-by-frame. Given the scarcity of experts' time, efficient annotation methods suitable for clinicians are needed. We propose an on-the-fly method for live video annotation to enhance the annotation efficiency. In this approach, a continuous single-point annotation is maintained by keeping the cursor on the object in a live video, mitigating the need for tedious pausing and repetitive navigation inherent in traditional annotation methods. This novel annotation paradigm inherits the point annotation's ability to generate pseudo-labels using a point-to-box teacher model. We empirically evaluate this approach by developing a dataset and comparing on-the-fly annotation time against traditional annotation method. Using our method, annotation speed was faster than the traditional annotation technique. We achieved a mean improvement of AP@50 over conventional method at equivalent annotation budgets on the developed dataset. Without bells and whistles, our approach offers a significant speed-up in annotation tasks. It can be easily implemented on any annotation platform to accelerate the integration of deep learning in video-based medical research.

End-to-End Phase Field Model Discovery Combining Experimentation, Crowdsourcing, Simulation and Learning

The availability of tera-byte scale experiment data calls for AI driven approaches which automatically discover scientific models from data. Nonetheless, significant challenges present in AI-driven scientific discovery: (i) The annotation of large scale datasets requires fundamental re-thinking in developing scalable crowdsourcing tools. (ii) The learning of scientific models from data calls for innovations beyond black-box neural nets. (iii) Novel visualization & diagnosis tools are needed for the collaboration of experimental and theoretical physicists, and computer scientists. We present Phase-Field-Lab platform for end-to-end phase field model discovery, which automatically discovers phase field physics models from experiment data, integrating experimentation, crowdsourcing, simulation and learning. Phase-Field-Lab combines (i) a streamlined annotation tool which reduces the annotation time (by ~50-75%), while increasing annotation accuracy compared to baseline; (ii) an end-to-end neural model which automatically learns phase field models from data by embedding phase field simulation and existing domain knowledge into learning; and (iii) novel interfaces and visualizations to integrate our platform into the scientific discovery cycle of domain scientists. Our platform is deployed in the analysis of nano-structure evolution in materials under extreme conditions (high temperature and irradiation). Our approach reveals new properties of nano-void defects, which otherwise cannot be detected via manual analysis.