Workflows for microscopy image analysis and cellular phenotyping

Thomas Wollmann; Holger Erfle; Roland Eils; Karl Rohr; Manuel Gunkel

doi:10.1016/j.jbiotec.2017.07.019

Workflows for microscopy image analysis and cellular phenotyping

J Biotechnol. 2017 Nov 10:261:70-75. doi: 10.1016/j.jbiotec.2017.07.019. Epub 2017 Jul 27.

Authors

Thomas Wollmann¹, Holger Erfle², Roland Eils³, Karl Rohr³, Manuel Gunkel²

Affiliations

¹ Dept. Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and DKFZ Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany. Electronic address: [email protected].
² High-Content Analysis of the Cell (HiCell) and ViroQuant-CellNetworks RNAi Screening Facility, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
³ Dept. Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BioQuant, IPMB, and DKFZ Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.

PMID: 28757289
DOI: 10.1016/j.jbiotec.2017.07.019

Abstract

In large scale biological experiments, like high-throughput or high-content cellular screening, the amount and the complexity of images to be analyzed are steadily increasing. To handle and process these images, well defined image processing and analysis steps need to be performed by applying dedicated workflows. Multiple software tools have emerged with the aim to facilitate creation of such workflows by integrating existing methods, tools, and routines, and by adapting them to different applications and questions, as well as making them reusable and interchangeable. In this review, we describe workflow systems for the integration of microscopy image analysis techniques with focus on KNIME and Galaxy.

Keywords: Galaxy; Image analysis; KNIME; Microscopy; Pipeline; Workflow; de.NBI.

Publication types

Review

MeSH terms

Computational Biology*
Cytological Techniques*
Image Processing, Computer-Assisted*
Microscopy*
Phenotype
Software
Workflow