Andy's Algorithms: new automated digital image analysis pipelines for FIJI.

Law, AMK; Yin, JXM; Castillo, L; Young, AIJ; Piggin, C; Rogers, S; Caldon, CE; Burgess, A; Millar, EKA; O'Toole, SA; Gallego-Ortega, D; Ormandy, CJ; Oakes, SR

Andy's Algorithms: new automated digital image analysis pipelines for FIJI.

Law, AMK Yin, JXM Castillo, L Young, AIJ Piggin, C Rogers, S Caldon, CE Burgess, A Millar, EKA O'Toole, SA Gallego-Ortega, D Ormandy, CJ Oakes, SR

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Publisher:: NATURE PUBLISHING GROUP
Publication Type:: Journal Article
Citation:: Sci Rep, 2017, 7, (1), pp. 15717
Issue Date:: 2017-11-16

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Field	Value	Language
dc.contributor.author	Law, AMK
dc.contributor.author	Yin, JXM
dc.contributor.author	Castillo, L
dc.contributor.author	Young, AIJ
dc.contributor.author	Piggin, C
dc.contributor.author	Rogers, S
dc.contributor.author	Caldon, CE
dc.contributor.author	Burgess, A
dc.contributor.author	Millar, EKA
dc.contributor.author	O'Toole, SA
dc.contributor.author	Gallego-Ortega, D
dc.contributor.author	Ormandy, CJ
dc.contributor.author	Oakes, SR
dc.date.accessioned	2022-04-13T12:24:43Z
dc.date.available	2017-10-31
dc.date.available	2022-04-13T12:24:43Z
dc.date.issued	2017-11-16
dc.identifier.citation	Sci Rep, 2017, 7, (1), pp. 15717
dc.identifier.issn	2045-2322
dc.identifier.issn	2045-2322
dc.identifier.uri	http://hdl.handle.net/10453/156216
dc.description.abstract	Quantification of cellular antigens and their interactions via antibody-based detection methods are widely used in scientific research. Accurate high-throughput quantitation of these assays using general image analysis software can be time consuming and challenging, particularly when attempted by users with limited image processing and analysis knowledge. To overcome this, we have designed Andy's Algorithms, a series of automated image analysis pipelines for FIJI, that permits rapid, accurate and reproducible batch-processing of 3,3'-diaminobenzidine (DAB) immunohistochemistry, proximity ligation assays (PLAs) and other common assays. Andy's Algorithms incorporates a step-by-step tutorial and optimization pipeline to make batch image analysis simple for the untrained user and adaptable across laboratories. Andy's algorithms provide a simpler, faster, standardized work flow compared to existing programs, while offering equivalent performance and additional features, in a free to use open-source application of FIJI. Andy's Algorithms are available at GitHub, publicly accessed at https://github.com/andlaw1841/Andy-s-Algorithm .
dc.format	Electronic
dc.language	eng
dc.publisher	NATURE PUBLISHING GROUP
dc.relation.ispartof	Sci Rep
dc.relation.isbasedon	10.1038/s41598-017-15885-6
dc.rights	info:eu-repo/semantics/openAccess
dc.subject.mesh	3,3'-Diaminobenzidine
dc.subject.mesh	Algorithms
dc.subject.mesh	Animals
dc.subject.mesh	Automation
dc.subject.mesh	Benchmarking
dc.subject.mesh	Breast Neoplasms
dc.subject.mesh	Colony-Forming Units Assay
dc.subject.mesh	Female
dc.subject.mesh	Humans
dc.subject.mesh	Image Processing, Computer-Assisted
dc.subject.mesh	Immunohistochemistry
dc.subject.mesh	Mice
dc.subject.mesh	Software
dc.subject.mesh	Tissue Array Analysis
dc.subject.mesh	Animals
dc.subject.mesh	Humans
dc.subject.mesh	Mice
dc.subject.mesh	Breast Neoplasms
dc.subject.mesh	3,3'-Diaminobenzidine
dc.subject.mesh	Tissue Array Analysis
dc.subject.mesh	Colony-Forming Units Assay
dc.subject.mesh	Immunohistochemistry
dc.subject.mesh	Algorithms
dc.subject.mesh	Automation
dc.subject.mesh	Image Processing, Computer-Assisted
dc.subject.mesh	Software
dc.subject.mesh	Benchmarking
dc.subject.mesh	Female
dc.title	Andy's Algorithms: new automated digital image analysis pipelines for FIJI.
dc.type	Journal Article
utslib.citation.volume	7
utslib.location.activity	England
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology/School of Biomedical Engineering
pubs.organisational-group	/University of Technology Sydney/Centre for Health Technologies (CHT)
utslib.copyright.status	open_access	*
dc.date.updated	2022-04-13T12:24:35Z
pubs.issue	1
pubs.publication-status	Published online
pubs.volume	7
utslib.citation.issue	1

Abstract:

Quantification of cellular antigens and their interactions via antibody-based detection methods are widely used in scientific research. Accurate high-throughput quantitation of these assays using general image analysis software can be time consuming and challenging, particularly when attempted by users with limited image processing and analysis knowledge. To overcome this, we have designed Andy's Algorithms, a series of automated image analysis pipelines for FIJI, that permits rapid, accurate and reproducible batch-processing of 3,3'-diaminobenzidine (DAB) immunohistochemistry, proximity ligation assays (PLAs) and other common assays. Andy's Algorithms incorporates a step-by-step tutorial and optimization pipeline to make batch image analysis simple for the untrained user and adaptable across laboratories. Andy's algorithms provide a simpler, faster, standardized work flow compared to existing programs, while offering equivalent performance and additional features, in a free to use open-source application of FIJI. Andy's Algorithms are available at GitHub, publicly accessed at https://github.com/andlaw1841/Andy-s-Algorithm .

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http://hdl.handle.net/10453/156216