title: A bioimage informatics platform for high-throughput embryo phenotyping.
abstract: High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene-phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest.
authors.forename: James M
authors.initials: JM
authors.lastname: Brown
authors.forename: Neil R
authors.initials: NR
authors.lastname: Horner
authors.forename: Thomas N
authors.initials: TN
authors.lastname: Lawson
authors.forename: Tanja
authors.initials: T
authors.lastname: Fiegel
authors.forename: Simon
authors.initials: S
authors.lastname: Greenaway
authors.forename: Hugh
authors.initials: H
authors.lastname: Morgan
authors.forename: Natalie
authors.initials: N
authors.lastname: Ring
authors.forename: Luis
authors.initials: L
authors.lastname: Santos
authors.forename: Duncan
authors.initials: D
authors.lastname: Sneddon
authors.forename: Lydia
authors.initials: L
authors.lastname: Teboul
authors.forename: Jennifer
authors.initials: J
authors.lastname: Vibert
authors.forename: Gagarine
authors.initials: G
authors.lastname: Yaikhom
authors.forename: Henrik
authors.initials: H
authors.lastname: Westerberg
authors.forename: Ann-Marie
authors.initials: AM
authors.lastname: Mallon
mesh_terms: D000818:Animals; D001331:Automation; D004622:Embryo, Mammalian / Q000000981:diagnostic imaging* / Q000502:physiology*; D057166:High-Throughput Screening Assays / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D051379:Mice; D008810:Mice, Inbred C57BL; D008817:Mice, Mutant Strains; D057054:Molecular Imaging / Q000295:instrumentation / Q000379:methods*; D010641:Phenotype; D012984:Software
keywords: automated analysis; bioimage informatics; embryonic phenotyping; high-throughput; image processing; software tools