scholarly journals Deep learning for bioimage analysis in developmental biology

Development ◽  
2021 ◽  
Vol 148 (18) ◽  
Author(s):  
Adrien Hallou ◽  
Hannah G. Yevick ◽  
Bianca Dumitrascu ◽  
Virginie Uhlmann
Keyword(s):  
Developmental Biology ◽  
Deep Learning ◽  
Open Source ◽  
State Of The Art ◽  
Biological Systems ◽  
Research Project ◽  
Space And Time ◽  
Complex Image ◽  
The Future ◽  
Bioimage Analysis

ABSTRACT Deep learning has transformed the way large and complex image datasets can be processed, reshaping what is possible in bioimage analysis. As the complexity and size of bioimage data continues to grow, this new analysis paradigm is becoming increasingly ubiquitous. In this Review, we begin by introducing the concepts needed for beginners to understand deep learning. We then review how deep learning has impacted bioimage analysis and explore the open-source resources available to integrate it into a research project. Finally, we discuss the future of deep learning applied to cell and developmental biology. We analyze how state-of-the-art methodologies have the potential to transform our understanding of biological systems through new image-based analysis and modelling that integrate multimodal inputs in space and time.

Vesseg: An Open-Source Tool for Deep Learning-Based Atherosclerotic Plaque Quantification in Histopathology Image

2021 ◽  
Author(s):  
J.M. Murray ◽  
P. Pfeffer ◽  
R. Seifert ◽  
A. Hermann ◽  
J. Handke ◽  
...  
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Atherosclerotic Plaque ◽  
State Of The Art ◽  
The Mean ◽  
Time Savings ◽  
Plaque Quantification ◽  
Atherosclerosis Research ◽  
Hematoxylin Eosin ◽  
Microscopy Images

Objective: Manual plaque segmentation in microscopy images is a time-consuming process in atherosclerosis research and potentially subject to unacceptable user-to-user variability and observer bias. We address this by releasing Vesseg a tool that includes state-of-the-art deep learning models for atherosclerotic plaque segmentation. Approach and Results: Vesseg is a containerized, extensible, open-source, and user-oriented tool. It includes 2 models, trained and tested on 1089 hematoxylin-eosin stained mouse model atherosclerotic brachiocephalic artery sections. The models were compared to 3 human raters. Vesseg can be accessed at https://vesseg .online or downloaded. The models show mean Soerensen-Dice scores of 0.91±0.15 for plaque and 0.97±0.08 for lumen pixels. The mean accuracy is 0.98±0.05. Vesseg is already in active use, generating time savings of >10 minutes per slide. Conclusions: Vesseg brings state-of-the-art deep learning methods to atherosclerosis research, providing drastic time savings, while allowing for continuous improvement of models and the underlying pipeline.

Motives and Methods for Quantitative FLOSS Research

2011 ◽  
pp. 282-293
Author(s):  
Megan Conklin
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Survey Data ◽  
Open Source Software ◽  
Quantitative Data ◽  
State Of The Art ◽  
Current State ◽  
The Future ◽  
Small Project

This chapter explores the motivations and methods for mining (collecting, aggregating, distributing, and analyzing) data about free/libre open source software (FLOSS) projects. It first explores why there is a need for this type of data. Then the chapter outlines the current state-of-the art in collecting and using quantitative data about FLOSS project, focusing especially on the three main types of FLOSS data that have been gathered to date: data from large forges, data from small project sets, and survey data. Finally, the chapter will describe some possible areas for improvement and recommendations for the future of FLOSS data collection.

scholarly journals On Empirically Examining The Effectiveness Of Deep Learning-Based Bug Localization Models

2021 ◽  
Author(s):  
Sravya Sravya ◽  
Andriy Miranskyy ◽  
Ayse Bener
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Open Source ◽  
State Of The Art ◽  
Bug Localization ◽  
Baseline Model ◽  
Software Developer ◽  
The Past ◽  
Software Bug ◽  
Better Than

Software Bug Localization involves a significant amount of time and effort on the part of the software developer. Many state-of-the-art bug localization models have been proposed in the past, to help developers localize bugs easily. However, none of these models meet the adoption thresholds of the software practitioner. Recently some deep learning-based models have been proposed, that have been shown to perform better than the state-of-the-art models. With this motivation, we experiment on Convolution Neural Networks (CNNs) to examine their effectiveness in localizing bugs. We also train a SimpleLogistic model as a baseline model for our experiments. We train both our models on five open source Java projects and compare their performance across the projects. Our experiments show that the CNN models perform better than the SimpleLogistic models in most of the cases, but do not meet the adoption criteria set by the practitioners.

scholarly journals Tracking cell lineages in 3D by incremental deep learning

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Ko Sugawara ◽  
Çağrı Çevrim ◽  
Michalis Averof
Keyword(s):  
Deep Learning ◽  
Incremental Learning ◽  
Cell Tracking ◽  
State Of The Art ◽  
Training Data ◽  
Cell Lineages ◽  
Incremental Approach ◽  
Powerful Approach ◽  
Cell Track ◽  
Bioimage Analysis

Deep learning is emerging as a powerful approach for bioimage analysis. Its use in cell tracking is limited by the scarcity of annotated data for the training of deep-learning models. Moreover, annotation, training, prediction, and proofreading currently lack a unified user interface. We present ELEPHANT, an interactive platform for 3D cell tracking that addresses these challenges by taking an incremental approach to deep learning. ELEPHANT provides an interface that seamlessly integrates cell track annotation, deep learning, prediction, and proofreading. This enables users to implement cycles of incremental learning starting from a few annotated nuclei. Successive prediction-validation cycles enrich the training data, leading to rapid improvements in tracking performance. We test the software’s performance against state-of-the-art methods and track lineages spanning the entire course of leg regeneration in a crustacean over 1 week (504 timepoints). ELEPHANT yields accurate, fully-validated cell lineages with a modest investment in time and effort.

scholarly journals A Controlled Benchmark of Video Violence Detection Techniques

Information ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 321
Author(s):  
Nicola Convertini ◽  
Vincenzo Dentamaro ◽  
Donato Impedovo ◽  
Giuseppe Pirlo ◽  
Lucia Sarcinella
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Detection Techniques ◽  
Detection Systems ◽  
Current State ◽  
Violence Detection ◽  
Learning Techniques ◽  
The Future ◽  
Feature Based ◽  
Art Techniques

This benchmarking study aims to examine and discuss the current state-of-the-art techniques for in-video violence detection, and also provide benchmarking results as a reference for the future accuracy baseline of violence detection systems. In this paper, the authors review 11 techniques for in-video violence detection. They re-implement five carefully chosen state-of-the-art techniques over three different and publicly available violence datasets, using several classifiers, all in the same conditions. The main contribution of this work is to compare feature-based violence detection techniques and modern deep-learning techniques, such as Inception V3.

scholarly journals On Empirically Examining The Effectiveness Of Deep Learning-Based Bug Localization Models

2021 ◽  
Author(s):  
Sravya Sravya ◽  
Andriy Miranskyy ◽  
Ayse Bener
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Open Source ◽  
State Of The Art ◽  
Bug Localization ◽  
Baseline Model ◽  
Software Developer ◽  
The Past ◽  
Software Bug ◽  
Better Than

Software Bug Localization involves a significant amount of time and effort on the part of the software developer. Many state-of-the-art bug localization models have been proposed in the past, to help developers localize bugs easily. However, none of these models meet the adoption thresholds of the software practitioner. Recently some deep learning-based models have been proposed, that have been shown to perform better than the state-of-the-art models. With this motivation, we experiment on Convolution Neural Networks (CNNs) to examine their effectiveness in localizing bugs. We also train a SimpleLogistic model as a baseline model for our experiments. We train both our models on five open source Java projects and compare their performance across the projects. Our experiments show that the CNN models perform better than the SimpleLogistic models in most of the cases, but do not meet the adoption criteria set by the practitioners.

scholarly journals SAIF: A Correction-Detection Deep-Learning Architecture for Personal Assistants

Sensors ◽  
2020 ◽  
Vol 20 (19) ◽  
pp. 5577
Author(s):  
Amos Azaria ◽  
Keren Nivasch
Keyword(s):  
Deep Learning ◽  
Natural Language ◽  
Intelligent Agents ◽  
State Of The Art ◽  
Intelligent Agent ◽  
Current State ◽  
The Future ◽  
Art Methods ◽  
Personal Assistants ◽  
Unique Dataset

Intelligent agents that can interact with users using natural language are becoming increasingly common. Sometimes an intelligent agent may not correctly understand a user command or may not perform it properly. In such cases, the user might try a second time by giving the agent another, slightly different command. Giving an agent the ability to detect such user corrections might help it fix its own mistakes and avoid making them in the future. In this work, we consider the problem of automatically detecting user corrections using deep learning. We develop a multimodal architecture called SAIF, which detects such user corrections, taking as inputs the user’s voice commands as well as their transcripts. Voice inputs allow SAIF to take advantage of sound cues, such as tone, speed, and word emphasis. In addition to sound cues, our model uses transcripts to determine whether a command is a correction to the previous command. Our model also obtains internal input from the agent, indicating whether the previous command was executed successfully or not. Finally, we release a unique dataset in which users interacted with an intelligent agent assistant, by giving it commands. This dataset includes labels on pairs of consecutive commands, which indicate whether the latter command is in fact a correction of the former command. We show that SAIF outperforms current state-of-the-art methods on this dataset.

scholarly journals Object Detection in Last Decade - A Survey

2021 ◽  
Vol 8 (1) ◽  
pp. 60-70
Author(s):  
Usama Arshad
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Face Detection ◽  
State Of The Art ◽  
Fundamental Problem ◽  
Research Work ◽  
Text Detection ◽  
Detection Techniques ◽  
The Future ◽  
Work Done

In the last decade, object detection is one of the interesting topics that played an important role in revolutionizing the presentera. Especially when it comes to computervision, object detection is a challenging and most fundamental problem. Researchersin the last decade enhanced object detection and made many advance discoveries using thetechnological advancements. When wetalk about object detection, we also must talk about deep learning and its advancements over the time. This research work describes theadvancements in object detection over last10 years (2010-2020). Different papers published in last 10 years related to objectdetection and its types are discussed with respect to their role in advancement of object detection. This research work also describesdifferent types of object detection, which include text detection, face detection etc. It clearly describes the changes inobject detection techniques over the period of the last 10 years. The Objectdetection is divided into two groups. General detectionand Task based detection. General detection is discussed chronologically and with its different variants while task based detectionincludes many state of the art algorithms and techniques according to tasks. Wealso described the basic comparison of how somealgorithms and techniques have been updated and played a major role in advancements of different fields related to object detection.We conclude that the most important advancements happened in the last decade and the future is promising much more advancement inobject detection on the basis of work done in this decade.In the last decade, object detection is one of the interesting topics that played an important role in revolutionizing the presentera. Especially when it comes to computervision, object detection is the challenging and most fundamental problem. Researchersinlast decade enhanced object detection and made many advance discoveries using thetechnological advancements. When wetalk about object detection, we also must talk about deep learning and its advancements over the time. This research work describes theadvancements in object detection over last10 years (2010-2020). Different papers published in last 10 years related to objectdetection and its types are discussed with respect to their role in advancement of object detection. This research work also describesdifferent types of object detection, which include text detection, face detection etc. It clearly describes the changes inobject detection techniques over the period of last 10 years. The Objectdetection is divided into two groups. General detectionand Task based detection. General detection is discussed chronologically and with its different variants while task based detectionincludes many state of the art algorithms and techniques according to tasks. Wealso described the basic comparison of how somealgorithms and techniques have been updated and played a major role in advancements of different fields related to object detection.We conclude that the most important advancements happened in last decade and future is promising much more advancement inobject detection on the basis of work done in this decade.

scholarly journals Open-source deep-learning software for bioimage segmentation

2021 ◽  
Vol 32 (9) ◽  
pp. 823-829
Author(s):  
Alice M. Lucas ◽  
Pearl V. Ryder ◽  
Bin Li ◽  
Beth A. Cimini ◽  
Kevin W. Eliceiri ◽  
...  
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Open Source Software ◽  
Learning Tools ◽  
Complex Information ◽  
Biological Structures ◽  
Bioimage Analysis ◽  
Learning Software ◽  
Dynamic Relationships ◽  
Microscopy Images

Microscopy images are rich in information about the dynamic relationships among biological structures. However, extracting this complex information can be challenging, especially when biological structures are closely packed, distinguished by texture rather than intensity, and/or low intensity relative to the background. By learning from large amounts of annotated data, deep learning can accomplish several previously intractable bioimage analysis tasks. Until the past few years, however, most deep-learning workflows required significant computational expertise to be applied. Here, we survey several new open-source software tools that aim to make deep-learning–based image segmentation accessible to biologists with limited computational experience. These tools take many different forms, such as web apps, plug-ins for existing imaging analysis software, and preconfigured interactive notebooks and pipelines. In addition to surveying these tools, we overview several challenges that remain in the field. We hope to expand awareness of the powerful deep-learning tools available to biologists for image analysis.

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