How to Do the Deconstruction of Bioimage Analysis Workflows: A Case Study with SurfCut-Reference-Cited by-同舟云学术

How to Do the Deconstruction of Bioimage Analysis Workflows: A Case Study with SurfCut

Published:2022 Issue: Volume: Page:115-146
ISSN:2509-6125
Container-title:Bioimage Data Analysis Workflows ‒ Advanced Components and Methods
language:
Short-container-title:

Author:

Louveaux Marion,Verger Stéphane

Abstract

AbstractPublished bioimage analysis workflows are designed for a specific biology use case and often hidden in the material and methods section of a biology paper. The art of the bioimage analyst is to find these workflows, deconstruct them and tune them to a new use case by replacing or modifying components of the workflow and/or linking them to other workflows.

Publisher

Springer International Publishing

Link

https://link.springer.com/content/pdf/10.1007/978-3-030-76394-7_6

Reference34 articles.

1. Arganda-Carreras I, Legland D, Rueden C, Mikushin D, Eglinger J, Burri O, Schindelin J, Helfrich S, Fiedler CC (2020) ijpb/MorphoLibJ: MorphoLibJ 1.4.2.1. https://doi.org/10.5281/zenodo.3826337

2. Band LR, Wells DM, Fozard JA, Ghetiu T, French AP, Pound MP, Wilson MH, Yu L, Li W, Hijazi HI, Oh J, Pearce SP, Perez-Amador MA, Yun J, Kramer E, Alonso JM, Godin C, Vernoux T, Hodgman TC, Pridmore TP, Swarup R, King JR, Bennett MJ (2014) Systems Analysis of Auxin Transport in the Arabidopsis Root Apex. Plant Cell 26(3):862–875. https://doi.org/10.1105/tpc.113.119495

3. Baral A, Aryal B, Jonsson K, Morris E, Demes E, Takatani S, Verger S, Xu T, Bennett M, Hamant O, Bhalerao RP (2021) External mechanical cues reveal a katanin-independent mechanism behind auxin-mediated tissue bending in plants. Dev Cell 56(1):67–80.e3, https://doi.org/10.1016/j.devcel.2020.12.008. https://linkinghub.elsevier.com/retrieve/pii/S1534580720309837

4. Boudaoud A, Burian A, Borowska-Wykret D, Uyttewaal M, Wrzalik R, Kwiatkowska D, Hamant O (2014) FibrilTool, an ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Nat Protoc 9(2):457–463. https://doi.org/10.1038/nprot.2014.024

5. Candeo A, Sana I, Ferrari E, Maiuri L, D’Andrea C, Valentini G, Bassi A (2016) Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine. J Biomed Optics 21(05):1. https://doi.org/10.1117/1.JBO.21.5.056001. https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-21/issue-05/056001/Virtual-unfolding-of-light-sheet-fluorescence-microscopy-dataset-for-quantitative/10.1117/1.JBO.21.5.056001.full

Cited by 2 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Multiscale mechanics drive functional maturation of the vertebrate heart;2024-07-24

2. High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress;BMC Biology;2023-07-10