Reproducible Experimental Design and Sample Prep
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Designing a rigorous microscopy experiment: Validating methods and avoiding bias
Jost AP, Waters JCJ Cell Biol. 2019 May 6;218(5):1452-1466. -
A biologist's guide to the field of quantitative bioimaging
BA Cimini et al -
FPbase: a community-editable fluorescent protein database
TJ. LambertNature Methods volume 16, pages277–278 (2019) -
Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design
Wait EC, Reiche MA, Chew TLJ Cell Sci. 2020 Nov 5;133(21) -
When light meets biology – how the specimen affects quantitative microscopy
Reiche MA, Aaron JS, Boehm U, DeSantis MC, Hobson CM, Khuon S, Lee RM, Chew TL.J Cell Sci. 2022 Mar 15;135(6) -
SearchLight Spectral Modeling & Analysis Tool
Detailed and Accurate methods reporting to improve reproducibility
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Best practices and tools for reporting reproducible fluorescence microscopy methods
P Montero Llopis et alNat Methods 18, 1463–1476 (2021). -
List of selected reagents, resources and initiatives in microscopy
Supplementary Information from P Montero Llopis et al, Nat Methods 18, 1463–1476 (2021). -
MicCheck - Microscopy Metadata Checklist Generator
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Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.
Rigano, A., Ehmsen, S., Öztürk, S.U. et al.Nat Methods 18, 1489–1495 (2021). https://doi.org/10.1038/s41592-021-01315-z -
MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text
Ryan, J., Pengo, T., Rigano, A. et al.Nat Methods 18, 1414–1416 (2021). -
MDEmic in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools
Kunis, S., Hänsch, S., Schmidt, C., & Wong, F.ArXiv. /abs/2103.02942 -
A guide to accurate reporting in digital image acquisition – can anyone replicate your microscopy data?
Heddleston JM, Aaron JS, Khuon S, Chew TLJ Cell Sci. 2021 Mar 30;134(6)
Data Visualization and Analysis
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Community-developed checklists for publishing images and image analysis
Schmied, C., Nelson, M., Avilov, S., Bakker, G., Bertocchi, C., Bischof, J., Boehm, U., Brocher, J., Carvalho, M., Chiritescu, C., Christopher, J., Cimini, B., Ebner, M., Ecker, R., Eliceiri, K., Gaudreault, N., Gelman, L., Grunwald, D., Gu, T., . . . JamArXiv. /abs/2302.07005 -
Effective image visualization for publications - a workflow using open access tools and concepts
Schmied C, Jambor HK.F1000Res. 2020 Nov 26;9:1373. -
Creating Clear and Informative Image-based Figures for Scientific Publications
Jambor HK. et al -
CyLinter
Baker, G. (2021)https://github.com/labsyspharm/cylinter -
BIAflows
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MCMICRO
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Believing is seeing - the deceptive influence of bias in quantitative microscopy