For investigations into fate specification and cell rearrangements in time-lapse images of preimplantation embryos, automated 3D instance segmentation of nuclei and subsequent nuclear tracking are invaluable. Often, the images' low signal-to-noise ratio and high voxel anisotropy and the nuclei's dense packing and variable shapes limit the performance of many segmentation methods, while subsequent tracking of nuclear instances is complicated by low frame rates and sample movements. Supervised machine learning approaches can radically improve segmentation accuracy and enable easier tracking, but they often require large amounts of difficult-to-obtain annotated 3D data. Here we report a novel mouse line expressing near-infrared nuclear reporter H2B-miRFP720. H2B-miRFP720 is the longest wavelength nuclear reporter in mice and can be imaged simultaneously with other reporters with minimal overlap. We then generate a dataset, which we call BlastoSPIM, of 3D microscopy images of H2B-miRFP720-expressing embryos with ground truth for nuclear instance segmentation. Using BlastoSPIM, we benchmark the performance of seven convolutional neural networks and identify Stardist-3D as the most accurate instance segmentation method across preimplantation development. We then construct a complete pipeline for nuclear instance segmentation with our BlastoSPIM-trained Stardist-3D models and lineage tracking from the 8-cell stage to the end of preimplantation development (>100 nuclei). Finally, we demonstrate BlastoSPIM's usefulness as pre-train data for related problems, both for a different imaging modality and for different model systems. BlastoSPIM, its corresponding Stardist-3D models, and documentation of the full associated analysis pipeline are available at: blastospim.flatironinstitute.org.

中文翻译：

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植入前小鼠胚胎的核实例分割和跟踪

对于研究植入前胚胎延时图像中的命运规范和细胞重排，细胞核的自动 3D 实例分割和随后的细胞核跟踪非常有价值。通常，图像的低信噪比和高体素各向异性以及核的密集堆积和可变形状限制了许多分割方法的性能，而随后的核实例跟踪由于低帧速率和样本移动而变得复杂。有监督的机器学习方法可以从根本上提高分割精度并更容易跟踪，但它们通常需要大量难以获得的带注释的 3D 数据。在这里，我们报道了一种表达近红外核报告基因 H2B-miRFP720 的新型小鼠品系。H2B-miRFP720 是小鼠中波长最长的核报告基因，可以与其他报告基因同时成像，重叠最小。然后，我们生成一个数据集（我们称之为 BlastoSPIM），其中包含表达 H2B-miRFP720 的胚胎的 3D 显微镜图像，并具有用于核实例分割的基本事实。使用 BlastoSPIM，我们对七个卷积神经网络的性能进行了基准测试，并将 Stardist-3D 确定为植入前开发中最准确的实例分割方法。然后，我们使用经过 BlastoSPIM 训练的 Stardist-3D 模型构建完整的核实例分割流程，并进行从 8 细胞阶段到植入前发育结束（> 100 个核）的谱系跟踪。最后，我们展示了 BlastoSPIM 作为相关问题的预训练数据的有用性，无论是针对不同的成像模式还是针对不同的模型系统。BlastoSPIM、其相应的 Stardist-3D 模型以及完整相关分析流程的文档可从以下网址获取：blastospim.flatironinstitute.org。