F1000research.com (11)#

Challenges and opportunities for bio-image analysis core-facilities#

Robert Haase

Licensed CC-BY-4.0

Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage

Content type: Slide

https://f1000research.com/slides/12-1054


Developing open-source software for bioimage analysis: opportunities and challenges#

Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase

Licensed CC-BY-4.0

This article outlines common challenges and practices when developing open-source software for bio-image analysis.

Tags: Neubias

Content type: Publication

https://f1000research.com/articles/10-302


EDAM-bioimaging: The ontology of bioimage informatics operations, topics, data, and formats (update 2020)#

Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A Kirschmann, Anatole Chessel, Leandro Scholz, Fabianne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux

Licensed CC-BY-4.0

Tags: Metadata

Content type: Publication, Poster

https://f1000research.com/posters/9-162


FAIRy deep-learning for bioImage analysis#

Estibaliz Gómez de Mariscal

Licensed CC-BY-4.0

Introduction to FAIR deep learning. Furthermore, tools to deploy trained DL models (deepImageJ), easily train and evaluate them (ZeroCostDL4Mic and DeepBacs) ensure reproducibility (DL4MicEverywhere), and share this technology in an open-source and reproducible manner (BioImage Model Zoo) are introduced.

Tags: Deep Learning, FAIR-Principles, Microscopy Image Analysis

Content type: Slides

https://f1000research.com/slides/13-147


Generative artificial intelligence for bio-image analysis#

Robert Haase

Licensed CC-BY-4.0

Tags: Python, Bioimage Analysis, Artificial Intelligence

Content type: Slide

https://f1000research.com/slides/12-971


Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists#

Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura

Published 2021

Licensed CC-BY-4.0

Tags: Bioimage Analysis, Neubias

Content type: Publication

https://f1000research.com/articles/10-334/v1


Hitchhiking through a diverse Bio-image Analysis Software Universe#

Robert Haase

Published 2022-07-22

Licensed CC-BY-4.0

Overview about decision making and how to influence decisions in the bio-image analysis software context.

Tags: Bioimage Analysis

Content type: Slide, Presentation

https://f1000research.com/slides/11-746

https://doi.org/10.7490/f1000research.1119026.1


Parallelization and heterogeneous computing: from pure CPU to GPU-accelerated image processing#

Robert Haase

Licensed CC-BY-4.0

Content type: Slide

https://f1000research.com/slides/11-1171

https://doi.org/10.7490/f1000research.1119154.1


Research data management for bioimaging - the 2021 NFDI4BIOIMAGE community survey#

Christian Schmidt, Janina Hanne, Josh Moore, Christian Meesters, Elisa Ferrando-May, et al.

Published 2022-09-20

Licensed CC-BY-4.0

As an initiative within Germany’s National Research Data Infrastructure, the authors conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs.

Tags: Research Data Management, Image Data Management, Bioimage Data

Content type: Publication

https://f1000research.com/articles/11-638/v2


Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey#

Christian Schmidt, Janina Hanne, Josh Moore, Christian Meesters, Elisa Ferrando-May, Stefanie Weidtkamp-Peters, members of the NFDI4BIOIMAGE initiative

Licensed CC-BY-4.0

Tags: Nfdi4Bioimage, Research Data Management

Content type: Publication

https://f1000research.com/articles/11-638


Sharing and licensing material#

Robert Haase

Licensed CC-BY-4.0

Introduction to sharing resources online and licensing

Tags: Sharing, Research Data Management

Content type: Slide

https://f1000research.com/slides/10-519