King's College London

Research portal

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

Research output: Contribution to journalReview articlepeer-review

Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer

Original languageEnglish
Pages (from-to)2472-2485
Number of pages14
JournalFEBS Letters
Volume596
Issue number19
DOIs
Accepted/In press2022
PublishedOct 2022

Bibliographical note

Funding Information: We would like to thank Mafalda Sousa (I3S, Porto), Ignacio Arganda‐Carreras (Universidad del Pais Vasco, Donostia‐San Sebastian), Martin Jones (The Francis Crick Institute, London) for reviewing the manuscript and providing constructive feedback prior to submission. We also would like to thank Michael Nelson (UW Madison), Sebastian Rhode (Zeiss), Ralph Palmisano (OICE Erlangen), Johannes Hohlbein (Wageningen UR), Kirti Prakash (ICR London) and Luciano Guerreiro Lucas (Leica Microsystems) for their constructive feedback about the preprint which we incorporated. RH acknowledges support by the Deutsche Forschungsgemeinschaft under Germany's Excellence Strategy – EXC2068 – Cluster of Excellence Physics of Life of TU Dresden. EF, IB and EJ acknowledge support by Biomedicum Imaging Unit and Electron Microscopy Unit, Helsinki University, as a part of Biocenter Finland infrastructure. CT acknowledges support by grant number 2020‐225265 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. SC acknowledges support from a Royal Society University Research Fellowship. AK was funded via the BioImage Informatics Facility, a unit of the National Bioinformatics Infrastructure Sweden NBIS, with funding from SciLifeLab, National Microscopy Infrastructure NMI (VR‐RFI 2019‐00217), and the Chan‐Zuckerberg Initiative. Open Access funding enabled and organized by Projekt DEAL. Funding Information: We would like to thank Mafalda Sousa (I3S, Porto), Ignacio Arganda-Carreras (Universidad del Pais Vasco, Donostia-San Sebastian), Martin Jones (The Francis Crick Institute, London) for reviewing the manuscript and providing constructive feedback prior to submission. We also would like to thank Michael Nelson (UW Madison), Sebastian Rhode (Zeiss), Ralph Palmisano (OICE Erlangen), Johannes Hohlbein (Wageningen UR), Kirti Prakash (ICR London) and Luciano Guerreiro Lucas (Leica Microsystems) for their constructive feedback about the preprint which we incorporated. RH acknowledges support by the Deutsche Forschungsgemeinschaft under Germany's Excellence Strategy – EXC2068 – Cluster of Excellence Physics of Life of TU Dresden. EF, IB and EJ acknowledge support by Biomedicum Imaging Unit and Electron Microscopy Unit, Helsinki University, as a part of Biocenter Finland infrastructure. CT acknowledges support by grant number 2020-225265 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. SC acknowledges support from a Royal Society University Research Fellowship. AK was funded via the BioImage Informatics Facility, a unit of the National Bioinformatics Infrastructure Sweden NBIS, with funding from SciLifeLab, National Microscopy Infrastructure NMI (VR-RFI 2019-00217), and the Chan-Zuckerberg Initiative. Open Access funding enabled and organized by Projekt DEAL. Publisher Copyright: © 2022 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

King's Authors

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.

View graph of relations

© 2020 King's College London | Strand | London WC2R 2LS | England | United Kingdom | Tel +44 (0)20 7836 5454