Images of mouse popliteal lymph node vascular structure derived using phase-contrast synchrotron micro-computed tomography (µCT)

This data record consists of a zipped folder LN image stacks.zip. The folder contains four other folders named LN1, LN2, LN3 and LN4 respectively. Each of these folders consists of a collection of images in .tif file format. These images were derived using phase-contrast synchrotron micro-computed tomography (µCT) and show details of lymph node (LN) vascular structure. Folders LN1-LN4 represent lymph node blood vessels of four mouse LNs that varied in overall nominal diameter from 1.0 – 1.4 mm.
The related study aimed to establish a corrosion casting
technique in combination with phase-contrast synchrotron micro-computed tomography (µCT) to quantify the details of lymph node vascular structure with the emphasis on the quantification of surface area distribution. By providing spatially-resolved 3D data on the distribution of blood vessels in lymph nodes, the eventual goal of the study was to understand LN transport phenomena down to the cell-level scale.
All experiments were undertaken with the approval of the Imperial College’s Animal Ethics Committee and were in accordance with its guidelines and the requirements of the United Kingdom Home Office regulations (ASPA 1986).
The blood in LN vasculature was flushed out and replaced with Mercox II resin to cast the lumen of the vasculature. The LN was then surgically excised and placed in a pipette tip before dissolving the tissue with potassium hydroxide. The freeze-dried samples were scanned with high-resolution synchrotron tomography and the radiographs were reconstructed into stack images using a phase-retrieval algorithm. The images were pre-processed by removing the pipette tip image using a cone crop before intensity-based segmentation and manual artefact processing. The binary data were then skeletonized and diameters and length of the vessels as well as the surface area density were calculated. Pressures and velocities of blood flow were estimated in each vessel based on an assumption of Poiseuille flow. The results were visualized with Imaris and further parameters quantified and plotted with Matlab. Please refer to the published article for more details on the methodology.

本数据集记录包含一个压缩文件夹“LN image stacks.zip”。该文件夹内包含四个子文件夹，分别命名为LN1、LN2、LN3与LN4。每个子文件夹均存储若干.tif格式的图像文件。这些图像由相衬同步辐射显微计算机断层扫描（phase-contrast synchrotron micro-computed tomography, µCT）采集得到，清晰呈现了淋巴结（lymph node, LN）的血管结构细节。LN1至LN4对应四只小鼠的淋巴结血管，这些淋巴结的标称总直径范围为1.0–1.4 mm。

本相关研究旨在建立一种结合相衬同步辐射显微计算机断层扫描（µCT）的腐蚀铸型技术，以量化淋巴结血管结构的细节，重点聚焦于血管表面积分布的定量分析。通过获取淋巴结血管分布的空间分辨三维数据，本研究的最终目标是在细胞尺度层面解析淋巴结的运输现象。

所有实验均获得帝国理工学院动物伦理委员会批准，并严格遵循其指南与英国内政部法规（ASPA 1986）的相关要求。

研究人员先将小鼠淋巴结血管内的血液冲洗干净，并用Mercox II树脂灌注以铸型血管腔。随后通过外科手术切除该淋巴结，将其置于移液管吸头中，再使用氢氧化钾溶解组织。经冷冻干燥处理后的样本通过高分辨率同步辐射断层扫描成像，利用相位恢复算法将射线底片重建为图像堆栈。预处理阶段，研究人员先通过锥形裁剪移除移液管吸头的图像，随后开展基于强度的分割与人工伪影处理。对得到的二值化数据进行骨架化处理后，计算血管的直径、长度以及表面积密度。基于泊肃叶流动假设，估算每根血管内的血流压力与流速。最终结果通过Imaris进行可视化，并借助Matlab完成剩余参数的量化与绘图。若需了解实验方法的更多细节，请参阅已发表的相关论文。