Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, United States.
Institute of Surgical Pathology, University of Freiburg, Faculty of Medicine, Freiburg 79106, Germany.
Bioinformatics. 2024 Nov 1;40(11). doi: 10.1093/bioinformatics/btae624.
Joint analysis of mass spectrometry images (MS images) and microscopy images of hematoxylin and eosin (H&E) stained tissues assists pathologists in characterizing the morphological structure of the tissues, and in performing diagnosis. Unfortunately, the analysis is undermined by substantial differences between these modalities in terms of aspect ratios, spatial resolution, number of channels in each image, as well as by large global or small local elastic spatial deformations of one image with respect to the other. Therefore, accurate coregistration of the images is a critical pre-requisite for their joint interpretation. We introduce MSIreg, an open-source R package for coregistration of MSI and H&E images. MSIreg is designed for high-dimensional MSI experiments where each spatial location is represented by thousands of mass features. Unlike most existing coregistration methods, MSIreg implements a landmark free workflow, and quantitative metrics for performance evaluation. We evaluate the performance of MSIreg on six case studies, including coregistration of contiguous tissues with large deformations, as well as simultaneous coregistration of 29 tissue microarray cores.
The R package, installation instructions, and fully reproducible vignettes describing methods and Case Studies are available open-source under the GPL-3.0 license at https://github.com/sslakkimsetty/msireg/.
对苏木精和伊红（H&E）染色组织的质谱成像（MS 图像）和显微镜图像进行联合分析，可以帮助病理学家描述组织的形态结构，并进行诊断。不幸的是，由于这些模态在纵横比、空间分辨率、每个图像的通道数量以及一个图像相对于另一个图像的全局或局部弹性空间变形方面存在很大差异，因此分析受到了严重影响。因此，对图像进行准确的配准是联合解释的关键前提。我们引入了 MSIreg，这是一个用于 MSI 和 H&E 图像配准的开源 R 包。MSIreg 专为高维 MSI 实验而设计，其中每个空间位置由数千个质量特征表示。与大多数现有的配准方法不同，MSIreg 实现了无地标工作流程，并具有用于性能评估的定量指标。我们在六个案例研究中评估了 MSIreg 的性能，包括具有大变形的连续组织的配准，以及 29 个组织微阵列核心的同时配准。
R 包、安装说明以及描述方法和案例研究的完全可重现简介可在 GPL-3.0 许可证下在 https://github.com/sslakkimsetty/msireg/ 上以开源方式获得。
