scholarly journals QuPath: Open source software for digital pathology image analysis

2017 ◽  
Author(s):  
Peter Bankhead ◽  
Maurice B Loughrey ◽  
José A Fernández ◽  
Yvonne Dombrowski ◽  
Darragh G McArt ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Digital Pathology ◽  
Tumor Identification ◽  
Wide Range ◽  
Slide Image ◽  
Bioimage Analysis ◽  
Additional Image ◽  
User Friendly ◽  
Biomarker Evaluation

AbstractQuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath’s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

Future of biomarker evaluation in the realm of artificial intelligence algorithms: application in improved therapeutic stratification of patients with breast and prostate cancer

2021 ◽  
pp. jclinpath-2020-207351
Author(s):  
Jenny Fitzgerald ◽  
Debra Higgins ◽  
Claudia Mazo Vargas ◽  
William Watson ◽  
Catherine Mooney ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Artificial Intelligence ◽  
Patient Outcome ◽  
Image Analysis ◽  
High Throughput Screening ◽  
Personalised Medicine ◽  
Digital Pathology ◽  
Disease Stage ◽  
Breast And Prostate Cancer ◽  
Biomarker Evaluation

Clinical workflows in oncology depend on predictive and prognostic biomarkers. However, the growing number of complex biomarkers contributes to costly and delayed decision-making in routine oncology care and treatment. As cancer is expected to rank as the leading cause of death and the single most important barrier to increasing life expectancy in the 21st century, there is a major emphasis on precision medicine, particularly individualisation of treatment through better prediction of patient outcome. Over the past few years, both surgical and pathology specialties have suffered cutbacks and a low uptake of pathology specialists means a solution is required to enable high-throughput screening and personalised treatment in this area to alleviate bottlenecks. Digital imaging in pathology has undergone an exponential period of growth. Deep-learning (DL) platforms for hematoxylin and eosin (H&E) image analysis, with preliminary artificial intelligence (AI)-based grading capabilities of specimens, can evaluate image characteristics which may not be visually apparent to a pathologist and offer new possibilities for better modelling of disease appearance and possibly improve the prediction of disease stage and patient outcome. Although digital pathology and AI are still emerging areas, they are the critical components for advancing personalised medicine. Integration of transcriptomic analysis, clinical information and AI-based image analysis is yet an uncultivated field by which healthcare professionals can make improved treatment decisions in cancer. This short review describes the potential application of integrative AI in offering better detection, quantification, classification, prognosis and prediction of breast and prostate cancer and also highlights the utilisation of machine learning systems in biomarker evaluation.

scholarly journals Droplet image analysis with user-friendly freeware CellProfiler

2020 ◽  
Vol 12 (17) ◽  
pp. 2287-2294
Author(s):  
Simona Bartkova ◽  
Marko Vendelin ◽  
Immanuel Sanka ◽  
Pille Pata ◽  
Ott Scheler
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
User Friendly ◽  
Free Open Source

We show how to use free open-source CellProfiler for droplet microfluidic image analysis.

scholarly journals Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

2021 ◽  
Vol 6 ◽  
pp. 76
Author(s):  
Mick A. Phillips ◽  
David Miguel Susano Pinto ◽  
Nicholas Hall ◽  
Julio Mateos-Langerak ◽  
Richard M. Parton ◽  
...  
Keyword(s):  
Open Source ◽  
Adaptive Optics ◽  
High Performance ◽  
Medical Science ◽  
Machine Learning Algorithms ◽  
Spatial Light Modulators ◽  
Structured Illumination ◽  
Light Modulators ◽  
Wide Range ◽  
User Friendly

We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.

scholarly journals MOSGA: Modular Open-Source Genome Annotator

2020 ◽  
Author(s):  
Roman Martin ◽  
Thomas Hackl ◽  
Georges Hattab ◽  
Matthias G Fischer ◽  
Dominik Heider
Keyword(s):  
Open Source ◽  
Source Code ◽  
Supplementary Information ◽  
Web Interface ◽  
Fully Integrated ◽  
Sequencing Technologies ◽  
A Genome ◽  
Wide Range ◽  
User Friendly ◽  
Eukaryotic Genomes

Abstract Motivation The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies—a crucial step toward unlocking the biology of the organism of interest—has remained a complex challenge that often requires advanced bioinformatics expertise. Results Here, we present MOSGA (Modular Open-Source Genome Annotator), a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. Availability and implementation We provide MOSGA as a web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga: latest. Source code can be found at https://gitlab.com/mosga/mosga Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals RhythmicAlly: Your R and Shiny–Based Open-Source Ally for the Analysis of Biological Rhythms

2019 ◽  
Vol 34 (5) ◽  
pp. 551-561 ◽  
Author(s):  
Lakshman Abhilash ◽  
Vasu Sheeba
Keyword(s):  
Time Series ◽  
Open Source ◽  
Time Series Data ◽  
Biological Rhythms ◽  
Series Data ◽  
Biological Time ◽  
Source Program ◽  
Wide Range ◽  
Infradian Rhythms ◽  
User Friendly

Research on circadian rhythms often requires researchers to estimate period, robustness/power, and phase of the rhythm. These are important to estimate, owing to the fact that they act as readouts of different features of the underlying clock. The commonly used tools, to this end, suffer from being very expensive, having very limited interactivity, being very cumbersome to use, or a combination of these. As a step toward remedying the inaccessibility to users who may not be able to afford them and to ease the analysis of biological time-series data, we have written RhythmicAlly, an open-source program using R and Shiny that has the following advantages: (1) it is free, (2) it allows subjective marking of phases on actograms, (3) it provides high interactivity with graphs, (4) it allows visualization and storing of data for a batch of individuals simultaneously, and (5) it does what other free programs do but with fewer mouse clicks, thereby being more efficient and user-friendly. Moreover, our program can be used for a wide range of ultradian, circadian, and infradian rhythms from a variety of organisms, some examples of which are described here. The first version of RhythmicAlly is available on Github, and we aim to maintain the program with subsequent versions having updated methods of visualizing and analyzing time-series data.

scholarly journals ARTIFICIAL INTELLIGENCE AND NEXT GENERATION PATHOLOGY: TOWARDS PERSONALIZED MEDICINE

2021 ◽  
Vol 65 (2) ◽  
Author(s):  
Oleksandr Dudin ◽  
◽  
Ozar Mintser ◽  
Oksana Sulaieva ◽  
◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Image Analysis ◽  
Deep Learning ◽  
Personalized Medicine ◽  
Digital Pathology ◽  
Automated Image Analysis ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Wide Range

Introduction. Over the past few decades, thanks to advances in algorithm development, the introduction of available computing power, and the management of large data sets, machine learning methods have become active in various fields of life. Among them, deep learning possesses a special place, which is used in many spheres of health care and is an integral part and prerequisite for the development of digital pathology. Objectives. The purpose of the review was to gather the data on existing image analysis technologies and machine learning tools developed for the whole-slide digital images in pathology. Methods: Analysis of the literature on machine learning methods used in pathology, staps of automated image analysis, types of neural networks, their application and capabilities in digital pathology was performed. Results. To date, a wide range of deep learning strategies have been developed, which are actively used in digital pathology, and demonstrated excellent diagnostic accuracy. In addition to diagnostic solutions, the integration of artificial intelligence into the practice of pathomorphological laboratory provides new tools for assessing the prognosis and prediction of sensitivity to different treatments. Conclusions: The synergy of artificial intelligence and digital pathology is a key tool to improve the accuracy of diagnostics, prognostication and personalized medicine facilitation

scholarly journals Orbit Image Analysis: An open-source whole slide image analysis tool

2020 ◽  
Vol 16 (2) ◽  
pp. e1007313 ◽  
Author(s):  
Manuel Stritt ◽  
Anna K. Stalder ◽  
Enrico Vezzali
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Analysis Tool ◽  
Whole Slide Image ◽  
Slide Image

scholarly journals Developing image analysis pipelines of whole-slide images: Pre- and post-processing

2020 ◽  
pp. 1-11
Author(s):  
Byron Smith ◽  
Meyke Hermsen ◽  
Elizabeth Lesser ◽  
Deepak Ravichandar ◽  
Walter Kremers
Keyword(s):  
Image Analysis ◽  
Deep Learning ◽  
Digital Pathology ◽  
Disruptive Technology ◽  
Post Processing ◽  
Artifact Detection ◽  
The Press ◽  
Slide Image ◽  
Processing Order ◽  
Whole Slide Images

Abstract Deep learning has pushed the scope of digital pathology beyond simple digitization and telemedicine. The incorporation of these algorithms in routine workflow is on the horizon and maybe a disruptive technology, reducing processing time, and increasing detection of anomalies. While the newest computational methods enjoy much of the press, incorporating deep learning into standard laboratory workflow requires many more steps than simply training and testing a model. Image analysis using deep learning methods often requires substantial pre- and post-processing order to improve interpretation and prediction. Similar to any data processing pipeline, images must be prepared for modeling and the resultant predictions need further processing for interpretation. Examples include artifact detection, color normalization, image subsampling or tiling, removal of errant predictions, etc. Once processed, predictions are complicated by image file size – typically several gigabytes when unpacked. This forces images to be tiled, meaning that a series of subsamples from the whole-slide image (WSI) are used in modeling. Herein, we review many of these methods as they pertain to the analysis of biopsy slides and discuss the multitude of unique issues that are part of the analysis of very large images.

scholarly journals QuPath: Open source software for digital pathology image analysis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Peter Bankhead ◽  
Maurice B. Loughrey ◽  
José A. Fernández ◽  
Yvonne Dombrowski ◽  
Darragh G. McArt ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Digital Pathology ◽  
Pathology Image
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