Domain-specific AI segmentation of IMPDH2 rod/ring structures in mouse embryonic stem cells.

IF 4.4 1区 生物学 Q1 BIOLOGY
Samuel T M Ball, Meagan J Hennessy, Yuhan Tan, Kai F Hoettges, Neil D Perkins, David J Wilkinson, Michael R H White, Yalin Zheng, David A Turner
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引用次数: 0

Abstract

Background: Inosine monophosphate dehydrogenase 2 (IMPDH2) is an enzyme that catalyses the rate-limiting step of guanine nucleotides. In mouse embryonic stem cells (ESCs), IMPDH2 forms large multi-protein complexes known as rod-ring (RR) structures that dissociate when ESCs differentiate. Manual analysis of RR structures from confocal microscopy images, although possible, is not feasible on a large scale due to the quantity of RR structures present in each field of view. To address this analysis bottleneck, we have created a fully automatic RR image classification pipeline to segment, characterise and measure feature distributions of these structures in ESCs.

Results: We find that this model can automatically segment images with a Dice score of over 80% for both rods and rings for in-domain images compared to expert annotation, with a slight drop to 70% for datasets out of domain. Important feature measurements derived from these segmentations show high agreement with the measurements derived from expert annotation, achieving an R2 score of over 90% for counting the number of RRs over the dataset.

Conclusions: We have established for the first time a quantitative baseline for RR distribution in pluripotent ESCs and have made a pipeline available for training to be applied to other models in which RR remain an open topic of study.

小鼠胚胎干细胞中IMPDH2棒/环结构的区域特异性AI分割。
背景:肌苷单磷酸脱氢酶2 (IMPDH2)是一种催化鸟嘌呤核苷酸限速步骤的酶。在小鼠胚胎干细胞(ESCs)中,IMPDH2形成被称为杆环(RR)结构的大型多蛋白复合物,当ESCs分化时解离。人工分析共聚焦显微镜图像中的RR结构虽然是可能的,但由于每个视场中存在大量的RR结构,因此在大范围内是不可行的。为了解决这一分析瓶颈,我们创建了一个全自动RR图像分类管道来分割、表征和测量ESCs中这些结构的特征分布。结果:我们发现,与专家注释相比,该模型可以自动分割图像,在域内图像中,棒和环的Dice得分都超过80%,对于域外数据集,该模型的Dice得分略降至70%。从这些分割中得出的重要特征测量结果与专家注释得出的测量结果高度一致,在计算数据集上rr的数量时,R2得分超过90%。结论:我们首次建立了多能性ESCs中RR分布的定量基线,并建立了一个可用于培训的管道,以应用于其他模型,其中RR仍然是一个开放的研究主题。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
BMC Biology
BMC Biology 生物-生物学
CiteScore
7.80
自引率
1.90%
发文量
260
审稿时长
3 months
期刊介绍: BMC Biology is a broad scope journal covering all areas of biology. Our content includes research articles, new methods and tools. BMC Biology also publishes reviews, Q&A, and commentaries.
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