A Hitchhiker's guide through the bio‐image analysis software universe

Abstract

Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualising information derived from microscopy imaging data of biological samples. In the past decade, we observed a dramatic increase in available software packages for these purposes. As it is increasingly difficult to keep track of the number of available image analysis platforms, tool collections, components and emerging technologies, we provide a conservative overview of software that we use in daily routine and give insights into emerging new tools. We give guidance on which aspects to consider when choosing the platform that best suits the user's needs, including aspects such as image data type, skills of the team, infrastructure and community at the institute and availability of time and budget.

Challenges and Opportunities for Bio-image Analysis Core-facilities

“…Staying up-to-date in the rapidly developing field of bio-image analysis is challenging. For example, deep learning and cloud computing are expected to have major impact on how computational resources are used in projects in the next 5-10 years [5]. Dedicated actions need to be undertaken by service-providing staff to determine which of the upcoming techniques are relevant for the institute, fulfill certain quality criteria and fit into the available computational infrastructure on campus.…”

“…Core-facility members maintaining a software-package also typically know it well and can teach it to a local community. As maintaining software and related knowledge can come at high costs, keeping the number of maintained and taught software applications small is key towards sustainable software and knowledge maintenance [5].…”

Microspectroscopy: functional imaging of biological systems

“…The wealth of different imaging systems is accompanied by an increasing number of software packages for the analysis of acquired images. Haase et al [2] have summarized a long list of currently available software tools for image analysis. IMAGE J (or FIJI) applications are discussed and tools to quantify the number of cells, and many other parameters are described.…”

“…Haase et al. [2] have summarized a long list of currently available software tools for image analysis. image j (or fiji ) applications are discussed and tools to quantify the number of cells, and many other parameters are described.…”

Applications of Deep Learning for Drug Discovery Systems with BigData

“…Therefore, "bioinformatics", which solves these problems using information science methods, has attracted much attention in recent years. Particularly in bioimaging, bioinformatics has been pushing forward and various research has been conducted, such as database development for biological images and the extraction of information from images, including the segmentation of cells and tissues, as well as the visualization of image information [26][27][28]. Among these, research on the classification and clustering of biological images using machine learning has been the most-studied area.…”