Reproducible image handling and analysis

No raw data, no science: another possible source of the reproducibility crisis

(2020) Tsuyoshi Miyakawa   Molecular Brain

Science Forum: Imaging methods are vastly underreported in biomedical research

(2020) Guillermo Marques et al.   eLife

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

(2019) Juan C. Caicedo et al.   CYTOMETRY PART A

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

The science institutions hiring integrity inspectors to vet their papers

(2019) Alison Abbott   NATURE

An empirical analysis of journal policy effectiveness for computational reproducibility

(2018) Victoria Stodden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

A call for public archives for biological image data

(2018) Jan Ellenberg et al.   NATURE METHODS

DeconvolutionLab2: An open-source software for deconvolution microscopy

(2017) Daniel Sage et al.   METHODS

The BioStudies database—one stop shop for all data supporting a life sciences study

(2017) Ugis Sarkans et al.   NUCLEIC ACIDS RESEARCH

Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators

(2017) Lindsay Barone et al.   PLoS Computational Biology

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

What does research reproducibility mean?

(2016) Steven N. Goodman et al.   Science Translational Medicine

When things go wrong: correcting the scientific record

(2015) B. Pulverer   EMBO JOURNAL

Image data in need of a home

(2015) T. Lemberger   Molecular Systems Biology

The inner centromere–shugoshin network prevents chromosomal instability

(2015) Yuji Tanno et al.   SCIENCE

The Economics of Reproducibility in Preclinical Research

(2015) Leonard P. Freedman et al.   PLOS BIOLOGY

ScientiFig: a tool to build publication-ready scientific figures

(2013) Benoit Aigouy et al.   NATURE METHODS

Manipulation and Misconduct in the Handling of Image Data

(2013) C. Martin et al.   PLANT CELL

Not seeing is not believing: improving the visibility of your fluorescence images

(2012) Jayme Johnson   MOLECULAR BIOLOGY OF THE CELL

Raise standards for preclinical cancer research

(2012) C. Glenn Begley et al.   NATURE

Annotated high-throughput microscopy image sets for validation

(2012) Vebjorn Ljosa et al.   NATURE METHODS

Icy: an open bioimage informatics platform for extended reproducible research

(2012) Fabrice de Chaumont et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

High-Content Phenotypic Profiling of Drug Response Signatures across Distinct Cancer Cells

(2010) P. D. Caie et al.   MOLECULAR CANCER THERAPEUTICS