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nf-core/mcmicro: Citations

nf-core

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

  • BaSiCPy

    Peng, T., Thorn, K., Schroeder, T., Wang, L., Theis, F. J., Marr, C., Navab, N. A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images. Nature Communication 2017 June 08; 8(1):14836. doi: 10.1038/ncomms14836.

  • ASHLAR

    Muhlich, J. L., Chen, Y., Yapp, C., Russell, D., Santagata, S., Sorger, P. K. Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. Bioinformatics 2022 October; 38(19):4613–4621. doi: 10.1093/bioinformatics/btac544.

  • Backsub

    Schapiro, D., Sokolov, A., Yapp, C. et al. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311–315. doi: 10.1038/s41592-021-01308-y

  • Coreograph

    Schapiro, D., Sokolov, A., Yapp, C. et al. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311–315. doi: 10.1038/s41592-021-01308-y

  • Cellpose

    Pachitariu, M., Stringer, C. Cellpose 2.0: how to train your own model. Nat Methods 2022; 19:1634–1641. doi: 10.1038/s41592-022-01663-4

  • Mesmer

    Greenwald, N.F., Miller, G., Moen, E. et al. Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. Nat Biotechnol 2022; 40:555–565. doi: 10.1038/s41587-021-01094-0

  • MCQuant

    Schapiro, D., Sokolov, A., Yapp, C. et al. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311–315. doi: 10.1038/s41592-021-01308-y

  • SciMap

    Nirmal et al. SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. Journal of Open Source Software 2024; 9(97):6604, doi: 10.21105/joss.06604

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

Software packaging/containerisation tools

  • Anaconda

    Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

  • Bioconda

    Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Docker

    Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

Test Data

Schapiro, D., Sokolov, A., Yapp, C. et al. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19:311–315. doi: 10.1038/s41592-021-01308-y