Data-archive to "Imaging the internal structure of Borelis schlumbergeri Reichel (1937): Advances by high-resolution hard X-ray tomography"

The internal structure of the extant larger benthic foraminifer Borelis schlumbergeri Reichel (1937) (Alveolinidae Ehrenberg, 1839) was investigated by high resolution hard x-ray computer tomography. Scanning was carried out using a single specimen using a Phoenix nanotom m from GE Sensing & Inspection Technologies GmbH. Exposure to hard x-rays was during about 4 hours and 1440 equiangular radiographs were taken along 360°. From the 2108 virtual slices through the stack visualizations of internal microstructures of the calcareous test and sarcode reconstruction were generated after segmentation and rendering in AVIZO7 software from FEI Visualization Sciences Group and using Voxler2 software from Golden Software, LLC. The 2.6 GB set including raw images, derived stacks of AVIZO labels, and video representations illustrating the interior of the Borelis specimen is put on line in form of a zipped archive for further experimentation by the community and for usage in micropaleontological training classes. The archive comprises the original stack of dicom images generated by the nanotom device, a reduced stack of derived AVIZO7 files and labels illustrating the reconstructed inner structures and rendered surfaces, a second reduced data stack of dicom images for loading and experimentation with ImageJ and Voxler2 software, an Excel-sheet containing volume measurements of individual segmented chambers and chamberlets.
In addition, several videos (GIF, AVI, MPEG) are provided illustrating the growth of the sarcode body from embryonic stage to adult stage, and showing the shell architecture of the investigated Borelis specimen in animated series of vertical slices.
Using the presented data requires access to AVIZO7 and / or Voxler2, which are commercial software. Alternatively, the provided stack of dicom images can also loaded and analyzed using open source Java plugins to ImageJ, which is in the public domain (https://imagej.net/). For visualization image stacks three-dimensionally and for volume rendering the ImageJ 3D Viewer plugin can be applied (http://3dviewer.neurofly.de), and segmentation of inner structures can be done using the Segmentation Editor in ImageJ from Johannes Schindelin, Francois Kusztos and Benjamin Schmid (https://imagej.net/Segmentation_Editor).

本研究采用高分辨率硬X射线计算机断层扫描（high resolution hard x-ray computer tomography）技术，对现生大型底栖有孔虫（larger benthic foraminifer）博列林氏有孔虫（Borelis schlumbergeri Reichel, 1937）（隶属于粟孔虫科（Alveolinidae Ehrenberg, 1839））的内部结构进行了探究。扫描实验采用单枚标本开展，设备为通用电气传感与检测技术有限公司（GE Sensing & Inspection Technologies GmbH）出品的Phoenix nanotom m型设备。本次硬X射线扫描时长约4小时，沿360°采集了1440幅等角度射线投影图。通过该扫描得到的2108层虚拟断层切片，经FEI可视化科学集团（FEI Visualization Sciences Group）的AVIZO7软件与Golden Software有限责任公司（Golden Software, LLC）的Voxler2软件进行分割与渲染后，生成了该有孔虫钙质壳体（calcareous test）内部微观结构以及肉足质（sarcode）的三维可视化重建结果。本数据集总容量为2.6 GB，包含原始扫描图像、AVIZO7标注派生数据栈以及展示该博列林氏有孔虫标本内部结构的可视化视频，以压缩归档形式上线，可供微古生物学领域同行开展后续实验研究，亦可用于微古生物学培训课程。该归档文件包含：纳米CT设备生成的原始DICOM图像栈；经简化的AVIZO7派生文件与标注数据栈，用于展示重建的内部结构与渲染后的壳体表面；第二套经简化的DICOM图像数据栈，可用于ImageJ与Voxler2软件的加载与实验分析；以及一份Excel表格，包含各分割房室及小房室的体积测量数据。
此外，本数据集还提供了多段视频（GIF、AVI、MPEG格式），分别展示了该有孔虫肉足体从胚胎期到成虫期的生长过程，以及以垂直切片动画序列形式呈现的标本壳体结构。
使用本数据集需配备AVIZO7与/或Voxler2商业软件。作为替代方案，提供的DICOM图像栈也可通过公有领域的开源软件ImageJ及其Java插件进行加载与分析（https://imagej.net/）。若需对图像栈进行三维可视化与体绘制，可使用ImageJ 3D查看器插件（ImageJ 3D Viewer plugin，http://3dviewer.neurofly.de）；内部结构的分割操作则可通过ImageJ内置的分割编辑器（Segmentation Editor）完成，该工具由Johannes Schindelin、Francois Kusztos与Benjamin Schmid开发（https://imagej.net/Segmentation_Editor）。