Replication Data for: "A probabilistic method for sampling α-shapes"

This repo contains two real datasets used in the manuscript entitled: "A probabilistic method for sampling α-shapes". In the first, we provide aligned CT scans of mandibular molars from two suborders of primates: Haplorhini (which include tarsiers and anthropoids) and Strepsirrhini (which include lemurs, galagos and lorises). From the haplorhine suborder, 7 molars came from the genus Tarsius; while, from the strepsirrhine suborder, 8 molars came from the genus Microcebus. For more information, also see Boyer et al. (2011) Anat Rec and Gao (2021) Appl Comput Harmon. In the second dataset, we provide binary masks for 22 septic, unstimulated neutrophils and 21 healthy, unstimulated neutrophils. Whole blood was obtained from healthy or septic donors with written informed consent and in accordance with the guidelines from and approval from the Rhode Island Hospital Institutional Review Board. Blood was collected in EDTA-containing Vacutainer tubes and separated by Histopaque-1077, followed by a sedimentation step with 3% 400–500 kDa Dextran. Contaminating erythrocytes were then removed via hypotonic lysis, and neutrophils were resuspended in cation-free HBSS. Neutrophils were photographed in polyacrylamide gels of 1.5 kPa stiffness and then their shapes were manually traced before being converted to segmented images. More details on the procedure are available in the manuscript as well as Witt et al (2023) Sci Rep.

本仓库包含收录于题为《α形状采样的概率方法》的手稿中的两组真实数据集。第一组数据集为两类灵长目亚目下颌磨牙的对齐CT扫描（Computed Tomography）图像：分别为简鼻亚目（Haplorhini，包含跗猴与类人猿）与原猴亚目（Strepsirrhini，包含狐猴、丛猴与懒猴）。其中简鼻亚目样本取自跗猴属（Tarsius），共7颗磨牙；原猴亚目样本取自倭狐猴属（Microcebus），共8颗磨牙。更多相关细节可参阅Boyer等人（2011）发表于《解剖学记录（Anat Rec）》的研究，以及Gao（2021）发表于《应用计算谐波分析（Appl Comput Harmon）》的成果。第二组数据集包含22张脓毒症状态下未受刺激中性粒细胞与21张健康状态下未受刺激中性粒细胞的二值掩码。全血样本取自签署书面知情同意书的健康或脓毒症志愿者，且所有实验流程均符合罗德岛医院机构审查委员会（Rhode Island Hospital Institutional Review Board）的指南与审批要求。血液采集于含乙二胺四乙酸（EDTA）的真空采血管（Vacutainer tubes）中，经Histopaque-1077试剂分离后，采用3%分子量为400–500 kDa的葡聚糖（Dextran）进行沉降处理。随后通过低渗裂解去除污染的红细胞，并用无阳离子的汉克斯平衡盐溶液（HBSS）重悬中性粒细胞。将中性粒细胞置于刚度为1.5 kPa的聚丙烯酰胺凝胶中进行拍摄，再手动勾勒其细胞形态并转换为分割图像。相关实验流程的更多细节可参阅本手稿以及Witt等人（2023）发表于《科学报告（Sci Rep）》的研究。