scholarly journals TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics

2021 ◽  
Author(s):  
Johnathan Pocock ◽  
Simon Graham ◽  
Quoc Dang Vu ◽  
Mostafa Jahanifar ◽  
Srijay Deshpande ◽  
...  

Computational Pathology (CPath) has seen rapid growth in recent years, driven by advanced deep learning (DL) algorithms. These algorithms typically share the same sequence of steps. However, due to the sheer size and complexity of handling large multi-gigapixel whole-slide images, there is no open-source software library that provides a generic end-to-end API for pathology image analysis using best practices for CPath. Most researchers have designed custom pipelines from the bottom-up, restricting the development of advanced CPath algorithms to specialist users. To help overcome this bottleneck, we present TIAToolbox, a Python toolbox designed to make CPath more accessible to new and advanced CPath scientists and pathologists alike. We provide a usable and adaptable library with efficient, cutting-edge and unit-tested tools for data loading, pre-processing, model inference, post-processing and visualization. This enables all kinds of users to easily build upon recent DL developments in the CPath literature. TIAToolbox provides a user-friendly modular API to enable seamless integration of advanced DL algorithms. We show with the help of examples how state-of-the-art DL algorithms can be streamlined using TIAToolbox.

2021 ◽  
Author(s):  
Brendon Lutnick ◽  
David Manthey ◽  
Jan Becker ◽  
Brandon Ginley ◽  
Katharina Moos ◽  
...  

Abstract We have developed Histo-Cloud, a tool for segmentation of whole slide images (WSIs) that has an easy-to-use graphical user interface. This tool runs a state-of-the-art convolutional neural network (CNN) for segmentation of WSIs in the cloud and allows the extraction of features from segmented regions for further analysis. By segmenting glomeruli, interstitial fibrosis and tubular atrophy, and vascular structures from renal and non-renal WSIs, we demonstrate the scalability, best practices for transfer learning, and effects of dataset variability. Finally, we demonstrate an application for animal model research, analyzing glomerular features in murine models of aging, diabetic nephropathy, and HIV associated nephropathy. The ability to access this tool over the internet will facilitate widespread use by computational non-experts. Histo-Cloud is open source and adaptable for segmentation of any histological structure regardless of stain.


2020 ◽  
Vol 2020 (10) ◽  
pp. 64-1-64-5
Author(s):  
Mustafa I. Jaber ◽  
Christopher W. Szeto ◽  
Bing Song ◽  
Liudmila Beziaeva ◽  
Stephen C. Benz ◽  
...  

In this paper, we propose a patch-based system to classify non-small cell lung cancer (NSCLC) diagnostic whole slide images (WSIs) into two major histopathological subtypes: adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). Classifying patients accurately is important for prognosis and therapy decisions. The proposed system was trained and tested on 876 subtyped NSCLC gigapixel-resolution diagnostic WSIs from 805 patients – 664 in the training set and 141 in the test set. The algorithm has modules for: 1) auto-generated tumor/non-tumor masking using a trained residual neural network (ResNet34), 2) cell-density map generation (based on color deconvolution, local drain segmentation, and watershed transformation), 3) patch-level feature extraction using a pre-trained ResNet34, 4) a tower of linear SVMs for different cell ranges, and 5) a majority voting module for aggregating subtype predictions in unseen testing WSIs. The proposed system was trained and tested on several WSI magnifications ranging from x4 to x40 with a best ROC AUC of 0.95 and an accuracy of 0.86 in test samples. This fully-automated histopathology subtyping method outperforms similar published state-of-the-art methods for diagnostic WSIs.


2021 ◽  
Vol 11 (15) ◽  
pp. 6975
Author(s):  
Tao Zhang ◽  
Lun He ◽  
Xudong Li ◽  
Guoqing Feng

Lipreading aims to recognize sentences being spoken by a talking face. In recent years, the lipreading method has achieved a high level of accuracy on large datasets and made breakthrough progress. However, lipreading is still far from being solved, and existing methods tend to have high error rates on the wild data and have the defects of disappearing training gradient and slow convergence. To overcome these problems, we proposed an efficient end-to-end sentence-level lipreading model, using an encoder based on a 3D convolutional network, ResNet50, Temporal Convolutional Network (TCN), and a CTC objective function as the decoder. More importantly, the proposed architecture incorporates TCN as a feature learner to decode feature. It can partly eliminate the defects of RNN (LSTM, GRU) gradient disappearance and insufficient performance, and this yields notable performance improvement as well as faster convergence. Experiments show that the training and convergence speed are 50% faster than the state-of-the-art method, and improved accuracy by 2.4% on the GRID dataset.


Semantic Web ◽  
2021 ◽  
pp. 1-16
Author(s):  
Esko Ikkala ◽  
Eero Hyvönen ◽  
Heikki Rantala ◽  
Mikko Koho

This paper presents a new software framework, Sampo-UI, for developing user interfaces for semantic portals. The goal is to provide the end-user with multiple application perspectives to Linked Data knowledge graphs, and a two-step usage cycle based on faceted search combined with ready-to-use tooling for data analysis. For the software developer, the Sampo-UI framework makes it possible to create highly customizable, user-friendly, and responsive user interfaces using current state-of-the-art JavaScript libraries and data from SPARQL endpoints, while saving substantial coding effort. Sampo-UI is published on GitHub under the open MIT License and has been utilized in several internal and external projects. The framework has been used thus far in creating six published and five forth-coming portals, mostly related to the Cultural Heritage domain, that have had tens of thousands of end-users on the Web.


Author(s):  
Yannick van Hierden ◽  
Timo Dietrich ◽  
Sharyn Rundle-Thiele

In recent years, the relevance of eHealth interventions has become increasingly evident. However, a sequential procedural application to cocreating eHealth interventions is currently lacking. This paper demonstrates the implementation of a participatory design (PD) process to inform the design of an eHealth intervention aiming to enhance well-being. PD sessions were conducted with 57 people across four sessions. Within PD sessions participants experienced prototype activities, provided feedback and designed program interventions. A 5-week eHealth well-being intervention focusing on lifestyle, habits, physical activity, and meditation was proposed. The program is suggested to be delivered through online workshops and online community interaction. A five-step PD process emerged; namely, (1) collecting best practices, (2) participatory discovery, (3) initial proof-of-concept, (4) participatory prototyping, and (5) pilot intervention proof-of-concept finalisation. Health professionals, behaviour change practitioners and program planners can adopt this process to ensure end-user cocreation using the five-step process. The five-step PD process may help to create user-friendly programs.


Author(s):  
Yuheng Hu ◽  
Yili Hong

Residents often rely on newspapers and television to gather hyperlocal news for community awareness and engagement. More recently, social media have emerged as an increasingly important source of hyperlocal news. Thus far, the literature on using social media to create desirable societal benefits, such as civic awareness and engagement, is still in its infancy. One key challenge in this research stream is to timely and accurately distill information from noisy social media data streams to community members. In this work, we develop SHEDR (social media–based hyperlocal event detection and recommendation), an end-to-end neural event detection and recommendation framework with a particular use case for Twitter to facilitate residents’ information seeking of hyperlocal events. The key model innovation in SHEDR lies in the design of the hyperlocal event detector and the event recommender. First, we harness the power of two popular deep neural network models, the convolutional neural network (CNN) and long short-term memory (LSTM), in a novel joint CNN-LSTM model to characterize spatiotemporal dependencies for capturing unusualness in a region of interest, which is classified as a hyperlocal event. Next, we develop a neural pairwise ranking algorithm for recommending detected hyperlocal events to residents based on their interests. To alleviate the sparsity issue and improve personalization, our algorithm incorporates several types of contextual information covering topic, social, and geographical proximities. We perform comprehensive evaluations based on two large-scale data sets comprising geotagged tweets covering Seattle and Chicago. We demonstrate the effectiveness of our framework in comparison with several state-of-the-art approaches. We show that our hyperlocal event detection and recommendation models consistently and significantly outperform other approaches in terms of precision, recall, and F-1 scores. Summary of Contribution: In this paper, we focus on a novel and important, yet largely underexplored application of computing—how to improve civic engagement in local neighborhoods via local news sharing and consumption based on social media feeds. To address this question, we propose two new computational and data-driven methods: (1) a deep learning–based hyperlocal event detection algorithm that scans spatially and temporally to detect hyperlocal events from geotagged Twitter feeds; and (2) A personalized deep learning–based hyperlocal event recommender system that systematically integrates several contextual cues such as topical, geographical, and social proximity to recommend the detected hyperlocal events to potential users. We conduct a series of experiments to examine our proposed models. The outcomes demonstrate that our algorithms are significantly better than the state-of-the-art models and can provide users with more relevant information about the local neighborhoods that they live in, which in turn may boost their community engagement.


2022 ◽  
Vol 18 (1) ◽  
pp. 1-41
Author(s):  
Pamela Bezerra ◽  
Po-Yu Chen ◽  
Julie A. McCann ◽  
Weiren Yu

As sensor-based networks become more prevalent, scaling to unmanageable numbers or deployed in difficult to reach areas, real-time failure localisation is becoming essential for continued operation. Network tomography, a system and application-independent approach, has been successful in localising complex failures (i.e., observable by end-to-end global analysis) in traditional networks. Applying network tomography to wireless sensor networks (WSNs), however, is challenging. First, WSN topology changes due to environmental interactions (e.g., interference). Additionally, the selection of devices for running network monitoring processes (monitors) is an NP-hard problem. Monitors observe end-to-end in-network properties to identify failures, with their placement impacting the number of identifiable failures. Since monitoring consumes more in-node resources, it is essential to minimise their number while maintaining network tomography’s effectiveness. Unfortunately, state-of-the-art solutions solve this optimisation problem using time-consuming greedy heuristics. In this article, we propose two solutions for efficiently applying Network Tomography in WSNs: a graph compression scheme, enabling faster monitor placement by reducing the number of edges in the network, and an adaptive monitor placement algorithm for recovering the monitor placement given topology changes. The experiments show that our solution is at least 1,000× faster than the state-of-the-art approaches and efficiently copes with topology variations in large-scale WSNs.


2020 ◽  
Author(s):  
Charly Empereur-mot ◽  
Luca Pesce ◽  
Davide Bochicchio ◽  
Claudio Perego ◽  
Giovanni M. Pavan

We present Swarm-CG, a versatile software for the automatic parametrization of bonded parameters in coarse-grained (CG) models. By coupling state-of-the-art metaheuristics to Boltzmann inversion, Swarm-CG performs accurate parametrization of bonded terms in CG models composed of up to 200 pseudoatoms within 4h-24h on standard desktop machines, using an AA trajectory as reference and default<br>settings of the software. The software benefits from a user-friendly interface and two different usage modes (default and advanced). We particularly expect Swarm-CG to support and facilitate the development of new CG models for the study of molecular systems interesting for bio- and nanotechnology.<br>Excellent performances are demonstrated using a benchmark of 9 molecules of diverse nature, structural complexity and size. Swarm-CG usage is ideal in combination with popular CG force<br>fields, such as e.g. MARTINI. However, we anticipate that in principle its versatility makes it well suited for the optimization of models built based also on other CG schemes. Swarm-CG is available with all its dependencies via the Python Package Index (PIP package: swarm-cg). Tutorials and demonstration data are available at: www.github.com/GMPavanLab/SwarmCG.


Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1824
Author(s):  
Pedro Albuquerque ◽  
João Pedro Machado ◽  
Tanmay Tulsidas Verlekar ◽  
Paulo Lobato Correia ◽  
Luís Ducla Soares

Several pathologies can alter the way people walk, i.e., their gait. Gait analysis can be used to detect such alterations and, therefore, help diagnose certain pathologies or assess people’s health and recovery. Simple vision-based systems have a considerable potential in this area, as they allow the capture of gait in unconstrained environments, such as at home or in a clinic, while the required computations can be done remotely. State-of-the-art vision-based systems for gait analysis use deep learning strategies, thus requiring a large amount of data for training. However, to the best of our knowledge, the largest publicly available pathological gait dataset contains only 10 subjects, simulating five types of gait. This paper presents a new dataset, GAIT-IT, captured from 21 subjects simulating five types of gait, at two severity levels. The dataset is recorded in a professional studio, making the sequences free of background camouflage, variations in illumination and other visual artifacts. The dataset is used to train a novel automatic gait analysis system. Compared to the state-of-the-art, the proposed system achieves a drastic reduction in the number of trainable parameters, memory requirements and execution times, while the classification accuracy is on par with the state-of-the-art. Recognizing the importance of remote healthcare, the proposed automatic gait analysis system is integrated with a prototype web application. This prototype is presently hosted in a private network, and after further tests and development it will allow people to upload a video of them walking and execute a web service that classifies their gait. The web application has a user-friendly interface usable by healthcare professionals or by laypersons. The application also makes an association between the identified type of gait and potential gait pathologies that exhibit the identified characteristics.


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