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Roston RA, Whikehart SM, Rolfe SM, Maga M. Morphological simulation tests the limits on phenotype discovery in 3D image analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.30.601430. [PMID: 39005442 PMCID: PMC11244899 DOI: 10.1101/2024.06.30.601430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In the past few decades, advances in 3D imaging have created new opportunities for reverse genetic screens. Rapidly growing datasets of 3D images of genetic knockouts require high-throughput, automated computational approaches for identifying and characterizing new phenotypes. However, exploratory, discovery-oriented image analysis pipelines used to discover these phenotypes can be difficult to validate because, by their nature, the expected outcome is not known a priori . Introducing known morphological variation through simulation can help distinguish between real phenotypic differences and random variation; elucidate the effects of sample size; and test the sensitivity and reproducibility of morphometric analyses. Here we present a novel approach for 3D morphological simulation that uses open-source, open-access tools available in 3D Slicer, SlicerMorph, and Advanced Normalization Tools in R (ANTsR). While we focus on diffusible-iodine contrast-enhanced micro-CT (diceCT) images, this approach can be used on any volumetric image. We then use our simulated datasets to test whether tensor-based morphometry (TBM) can recover our introduced differences; to test how effect size and sample size affect detectability; and to determine the reproducibility of our results. In our approach to morphological simulation, we first generate a simulated deformation based on a reference image and then propagate this deformation to subjects using inverse transforms obtained from the registration of subjects to the reference. This produces a new dataset with a shifted population mean while retaining individual variability because each sample deforms more or less based on how different or similar it is from the reference. TBM is a widely-used technique that statistically compares local volume differences associated with local deformations. Our results showed that TBM recovered our introduced morphological differences, but that detectability was dependent on the effect size, the sample size, and the region of interest (ROI) included in the analysis. Detectability of subtle phenotypes can be improved both by increasing the sample size and by limiting analyses to specific body regions. However, it is not always feasible to increase sample sizes in screens of essential genes. Therefore, methodical use of ROIs is a promising way to increase the power of TBM to detect subtle phenotypes. Generating known morphological variation through simulation has broad applicability in developmental, evolutionary, and biomedical morphometrics and is a useful way to distinguish between a failure to detect morphological difference and a true lack of morphological difference. Morphological simulation can also be applied to AI-based supervised learning to augment datasets and overcome dataset limitations.
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Zekavat AR, Lioliou G, Roche I Morgó O, Maughan Jones C, Galea G, Maniou E, Doherty A, Endrizzi M, Astolfo A, Olivo A, Hagen C. Phase contrast micro-CT with adjustable in-slice spatial resolution at constant magnification. Phys Med Biol 2024; 69:105017. [PMID: 38631365 DOI: 10.1088/1361-6560/ad4000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Objective.To report on a micro computed tomography (micro-CT) system capable of x-ray phase contrast imaging and of increasing spatial resolution at constant magnification.Approach.The micro-CT system implements the edge illumination (EI) method, which relies on two absorbing masks with periodically spaced transmitting apertures in the beam path; these split the beam into an array of beamlets and provide sensitivity to the beamlets' directionality, i.e. refraction. In EI, spatial resolution depends on the width of the beamlets rather than on the source/detector point spread function (PSF), meaning that resolution can be increased by decreasing the mask apertures, without changing the source/detector PSF or the magnification.Main results.We have designed a dedicated mask featuring multiple bands with differently sized apertures and used this to demonstrate that resolution is a tuneable parameter in our system, by showing that increasingly small apertures deliver increasingly detailed images. Phase contrast images of a bar pattern-based resolution phantom and a biological sample (a mouse embryo) were obtained at multiple resolutions.Significance.The new micro-CT system could find application in areas where phase contrast is already known to provide superior image quality, while the added tuneable resolution functionality could enable more sophisticated analyses in these applications, e.g. by scanning samples at multiple scales.
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Affiliation(s)
- Amir Reza Zekavat
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Grammatiki Lioliou
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Oriol Roche I Morgó
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Charlotte Maughan Jones
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Gabriel Galea
- University College London, GOS Institute of Child Health, London, United Kingdom
| | - Eirini Maniou
- University College London, GOS Institute of Child Health, London, United Kingdom
| | - Adam Doherty
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Marco Endrizzi
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Alberto Astolfo
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Alessandro Olivo
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Charlotte Hagen
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
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Bai Y, Bentley L, Ma C, Naveenan N, Cleak J, Wu Y, Simon MM, Westerberg H, Cañas RC, Horner N, Pandey R, Paphiti K, Schulze U, Mianné J, Hough T, Teboul L, de Baaij JH, Cox RD. Cleft palate and minor metabolic disturbances in a mouse global Arl15 gene knockout. FASEB J 2023; 37:e23211. [PMID: 37773757 PMCID: PMC10631251 DOI: 10.1096/fj.202201918r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/27/2023] [Accepted: 09/08/2023] [Indexed: 10/01/2023]
Abstract
ARL15, a small GTPase protein, was linked to metabolic traits in association studies. We aimed to test the Arl15 gene as a functional candidate for metabolic traits in the mouse. CRISPR/Cas9 germline knockout (KO) of Arl15 showed that homozygotes were postnatal lethal and exhibited a complete cleft palate (CP). Also, decreased cell migration was observed from Arl15 KO mouse embryonic fibroblasts (MEFs). Metabolic phenotyping of heterozygotes showed that females had reduced fat mass on a chow diet from 14 weeks of age. Mild body composition phenotypes were also observed in heterozygous mice on a high-fat diet (HFD)/low-fat diet (LFD). Females on a HFD showed reduced body weight, gonadal fat depot weight and brown adipose tissue (BAT) weight. In contrast, in the LFD group, females showed increased bone mineral density (BMD), while males showed a trend toward reduced BMD. Clinical biochemistry analysis of plasma on HFD showed transient lower adiponectin at 20 weeks of age in females. Urinary and plasma Mg2+ concentrations were not significantly different. Our phenotyping data showed that Arl15 is essential for craniofacial development. Adult metabolic phenotyping revealed potential roles in brown adipose tissue and bone development.
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Affiliation(s)
- Ying Bai
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Liz Bentley
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Chao Ma
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - James Cleak
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Yixing Wu
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Michelle M Simon
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Henrik Westerberg
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Ramón Casero Cañas
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Neil Horner
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Rajesh Pandey
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Keanu Paphiti
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | | | - Joffrey Mianné
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Tertius Hough
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Lydia Teboul
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Jeroen H.F. de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Roger D. Cox
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
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Rolfe SM, Whikehart SM, Maga AM. Deep learning enabled multi-organ segmentation of mouse embryos. Biol Open 2023; 12:bio059698. [PMID: 36802342 PMCID: PMC9990908 DOI: 10.1242/bio.059698] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/23/2023] Open
Abstract
The International Mouse Phenotyping Consortium (IMPC) has generated a large repository of three-dimensional (3D) imaging data from mouse embryos, providing a rich resource for investigating phenotype/genotype interactions. While the data is freely available, the computing resources and human effort required to segment these images for analysis of individual structures can create a significant hurdle for research. In this paper, we present an open source, deep learning-enabled tool, Mouse Embryo Multi-Organ Segmentation (MEMOS), that estimates a segmentation of 50 anatomical structures with a support for manually reviewing, editing, and analyzing the estimated segmentation in a single application. MEMOS is implemented as an extension on the 3D Slicer platform and is designed to be accessible to researchers without coding experience. We validate the performance of MEMOS-generated segmentations through comparison to state-of-the-art atlas-based segmentation and quantification of previously reported anatomical abnormalities in a Cbx4 knockout strain. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- S. M. Rolfe
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - S. M. Whikehart
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - A. M. Maga
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
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Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, Cacheiro P, Frost A, Keskivali-Bond P, Vardal B, McCoy A, Cheng TK, Santos L, Wells S, Smedley D, Mallon AM, Parkinson H. The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. Nucleic Acids Res 2023; 51:D1038-D1045. [PMID: 36305825 PMCID: PMC9825559 DOI: 10.1093/nar/gkac972] [Citation(s) in RCA: 120] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/05/2022] [Accepted: 10/14/2022] [Indexed: 01/30/2023] Open
Abstract
The International Mouse Phenotyping Consortium (IMPC; https://www.mousephenotype.org/) web portal makes available curated, integrated and analysed knockout mouse phenotyping data generated by the IMPC project consisting of 85M data points and over 95,000 statistically significant phenotype hits mapped to human diseases. The IMPC portal delivers a substantial reference dataset that supports the enrichment of various domain-specific projects and databases, as well as the wider research and clinical community, where the IMPC genotype-phenotype knowledge contributes to the molecular diagnosis of patients affected by rare disorders. Data from 9,000 mouse lines and 750 000 images provides vital resources enabling the interpretation of the ignorome, and advancing our knowledge on mammalian gene function and the mechanisms underlying phenotypes associated with human diseases. The resource is widely integrated and the lines have been used in over 4,600 publications indicating the value of the data and the materials.
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Affiliation(s)
- Tudor Groza
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Federico Lopez Gomez
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamed Haseli Mashhadi
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Violeta Muñoz-Fuentes
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Osman Gunes
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Robert Wilson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anthony Frost
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | | | - Bora Vardal
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Aaron McCoy
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Tsz Kwan Cheng
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Luis Santos
- Research Data Team, The Turing Institute, 96 Euston Rd, London NW1 2DB, UK
| | - Sara Wells
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Ann-Marie Mallon
- Research Data Team, The Turing Institute, 96 Euston Rd, London NW1 2DB, UK
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
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Handschuh S, Glösmann M. Mouse embryo phenotyping using X-ray microCT. Front Cell Dev Biol 2022; 10:949184. [PMID: 36187491 PMCID: PMC9523164 DOI: 10.3389/fcell.2022.949184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Microscopic X-ray computed tomography (microCT) is a structural ex vivo imaging technique providing genuine isotropic 3D images from biological samples at micron resolution. MicroCT imaging is non-destructive and combines well with other modalities such as light and electron microscopy in correlative imaging workflows. Protocols for staining embryos with X-ray dense contrast agents enable the acquisition of high-contrast and high-resolution datasets of whole embryos and specific organ systems. High sample throughput is achieved with dedicated setups. Consequently, microCT has gained enormous importance for both qualitative and quantitative phenotyping of mouse development. We here summarize state-of-the-art protocols of sample preparation and imaging procedures, showcase contemporary applications, and discuss possible pitfalls and sources for artefacts. In addition, we give an outlook on phenotyping workflows using microscopic dual energy CT (microDECT) and tissue-specific contrast agents.
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MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data 2022; 9:230. [PMID: 35614082 PMCID: PMC9133120 DOI: 10.1038/s41597-022-01338-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022] Open
Abstract
Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).
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