title: Anima: modular workflow system for comprehensive image data analysis.
abstract: Modern microscopes produce vast amounts of image data, and computational methods are needed to analyze and interpret these data. Furthermore, a single image analysis project may require tens or hundreds of analysis steps starting from data import and pre-processing to segmentation and statistical analysis; and ending with visualization and reporting. To manage such large-scale image data analysis projects, we present here a modular workflow system called Anima. Anima is designed for comprehensive and efficient image data analysis development, and it contains several features that are crucial in high-throughput image data analysis: programing language independence, batch processing, easily customized data processing, interoperability with other software via application programing interfaces, and advanced multivariate statistical analysis. The utility of Anima is shown with two case studies focusing on testing different algorithms developed in different imaging platforms and an automated prediction of alive/dead C. elegans worms by integrating several analysis environments. Anima is a fully open source and available with documentation at www.anduril.org/anima.
authors.affiliation: Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki , Helsinki , Finland.
authors.forename: Ville
authors.initials: V
authors.lastname: Rantanen
authors.affiliation: Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki , Helsinki , Finland.
authors.forename: Miko
authors.initials: M
authors.lastname: Valori
authors.affiliation: Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki , Helsinki , Finland.
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi
keywords: automated analysis; high-throughput; image analysis; quantification; superplatform