LAMA: automated image analysis for the developmental phenotyping of mouse embryos

Abstract

Advanced 3D imaging modalities, such as micro computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of manpower and expertise. Thus, rapid automated annotation is critical to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline, which harnesses the large amount of wild type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and using it with LAMA show that we can uncover known and novel dysmorphology from two IMPC knockout lines.

Cleft palate and minor metabolic disturbances in a mouse global Arl15 gene knockout

“…In order to screen for other developmental phenotypes, Micro-CT data was manually analyzed using 3D Slicer software followed by a high throughput computational pipeline called LAMA. 22 Two wildtype embryos were used in the primary screen to identify phenotypes that are highly penetrant. From manual interrogation, the tongue of homozygous KO animals was hunched because the development of the mandible was delayed (Figure S4C).…”

Mouse embryo phenotyping using X-ray microCT

“…This makes the database a rich resource, which in future can be explored by new analysis tools such as modern deep learning segmentation routines. Very recently, the novel automated image analysis pipeline for mouse embryo phenotyping (LAMA) made use of the large amount of IMPC wild-type embryo control data to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity (Horner et al, 2021). Employing a novel anatomical E14.5 embryo atlas with LAMA, it was possible to expose both known and novel dysmorphologies from two IMPC knockout lines.…”

“…The largest amount of microCT data on mouse development has been generated for E15.5 and E18.5 (Dickinson et al, 2016). More recently automated analysis has been extended to E14.5 (Horner et al, 2021). In the IMPC screens, E15.5 embryos were imaged with a voxel size of ~13 µm and datasets were downsampled to ~28 µm before automated analysis (Wong et al, 2014), which allows to detect both gross and subtle phenotypes (Wong et al, 2014;Dickinson et al, 2016).…”

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

“…The International Mouse Phenotyping Consortium (IMPC, www.mousephenotype.org) was born out of a need to determine the relationship between genotype and phenotype with standardized phenotypic data. Using micro-computed tomography (µCT) and optical projection tomography, the consortium has studied the anatomy of mouse lines heterozygous or homozygous for a single gene mutation, particularly at embryonic day E9.5, E14.5-15.5, and E18.5 [15][16][17][18][19][20] .…”