A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications - Supplementary Data

Videos Video 1 A video going through the Z stack in single slices. This is a cross- sectional view of the XRH image stack along the XY plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue. Video 2 A video going through the Y stack in single slices. This is a cross- sectional view of the XRH image stack along the XZ plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue. Video 3 A video going through the X stack in single slices. This is a cross- sectional view of the XRH image stack along the YZ plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue. Video 4 3D X-ray histology (XRH) is a µCT -based workflow tailored to fit seamlessly into current histology workflows in biomedical and pre-clinical research, as well as clinical histopathology. Microanatomical detail can be captured from standard (non-stained) formalin-fixed and paraffin-embedded (FFPE) tissue blocks. Video 5 Average Intensity Projection (AIP) of the sample through the Histologically relevant plane. This is a 2D visualisation rendering the Average Intensity of 20x single XY slices along the z-axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue. Video 6 Maximum Intensity Projection (MIP) of the sample through the Histologically relevant plane. This is a 2D visualisation rendering the Maximum Intensity of 20x single XY slices along the z-axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue. Video 7 Standard deviation projection of the sample going through the histologically relevant plane. This is a 2D visualisation rendering the Standard Deviation of 20x single XY slices along the z- axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue. * Videos 5 -7 are also referred to as "thick-slice rolls" - Thick-slice rolling is a 2D thick-slice viewing that allows rolling of a pre-selected number of slices (n) along the z-axis of the 3D data. A single thick-slice roll forwards is accomplished by translating the thick-slice by one single slice forwards; that is moving forward by one (+1) slice from the first and nth element and reapplying the criteria or operations to the new slice sub-stack. The questionnaire used to collect feedback about the needs of the XRH community. Survey.docx Survey.pdf Exemplar report of a semi-automatically generated augmented PDF file that contain sample information, imaging settings, still images with descriptive figure legends, and links to corresponding online videos DEMO02019-FFPE_report_99EbPXG.pdf = = = = = = = = = = = = = = = = System performance data ZIP = = = = = = = = = = = = = = = = This ZIP file contains imaging data collected through different systems and setups at the XRH facility at the μ-VIS X-ray Imaging Centre at the University of Southampton for the purpose of acceptance and/or system performance characterisation. Below is an overview of the folder structure and its contents The following files are X-ray imaging data collected on September 28, 2017, using the Med-X system and a Jima phantom at 55 kV peak and 7 Watts. 20170928_MEDX_1642_JIMA_55kVp7W-2.tif 20170928_MEDX_1642_JIMA_55kVp7W.tif 20170928_MEDX_1642_JIMA_55kVp7W.tif.profile.xml This PDF document is related to a QRM MicroCT bar pattern phantom, and its specifications QRM-MicroCT-Barpattern-Phantom.pdf Graphs showing the calculated focal-spot size as a function of the X-ray power (W) for the Molybdenum rotating target calculated using Edge Modulation function testing. The performance is then compared with the performance of the Reflection target across the same range of powers. Raw data can be found in XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize folder. Test performed in July 2021. XRH_202107_MoRot-testing_EdgeModFunction-QRMrecons+RotReflCompar.png / XRH-XT-H-225-ST_FocalSpots This directory contains radiographic data collected using the XRH system with a JIMA phantom and MoRt (Molybdenum rotating), TT (Transmission), and Reflection targets. 20200113_XRH_Jima test MoRT 55kV 15W.tif, 20200113_XRH_Jima test MoRT 55kV 30W.tif, etc.: These files represent radiographs taken on January 13, 2020, using the XRH system, Jima phantom, MoRT target at 55 kVp and varying wattages. 20200207_XRH_JIMA 80kV TT1a.tif, 20200207_XRH_JIMA 80kV TT1b.tif, etc. Similar to the above, these files are from February 7, 2020, and use 80 kVp with a TT target. 20231115_XRH_reflW_80kVp6W.tif, 20231115_XRH_reflW_80kVp6W_02.tif, etc. These files are from November 15, 2023, and collected using the XRH system with a Reflection target at 80 kVp and 6 Watts. / XRH_QRM_Refl-vs-Rot-TargetComparison_SingleRadioFromCTs_5umPixelSize This directory contains single radiographs taken with a pixel size of 5 micrometers using the Molybdenum rotating (MoRt), and the Reflection target using tungsten (W) and Molybdenum (Mo) metals. / XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize This directory contains sinlge reconstruction slices of the setups mentioned above. Slices are exported from CT volumes and were used for the Edge Modulation function study. For interpretation of the filenames in the folders listed above please see below and refer to specific files and folders for detailed information and results related to each imaging session: <xx>kVp or <xx>kV :Imaging at a peak voltage of <xx> kVp. <y>W :Imaging at <y> Watts; "." is represented with "-"; i.e. 20210705_XRH_2766_PJB_TEST03552-EQPMT_W_6-9W is acquired using a power of 6.9 W MoRt, TT, Refl :Molybdenum, Transmission, and Reflection targets, respectively. _W_ and _Mo_ :Tungsten and Molybdenum target materials. _horiz :Reconstruction slices in line with the X-ray beam's propagation direction. _vert :Reconstruction slices normal to the X-ray beam's propagation direction and parallel to the detector plane.Videos 视频1：以单切片序列遍历Z轴堆栈的视频。该视频为X射线组织学（X-ray histology, XRH）图像堆栈沿XY平面的横截面视图。XRH数据集通常会经过方向调整（重切片），使得沿XY平面滚动堆栈的操作可模拟组织的物理组织学切片过程。 视频2：以单切片序列遍历Y轴堆栈的视频。该视频为XRH图像堆栈沿XZ平面的横截面视图。XRH数据集通常会经过方向调整（重切片），使得沿XY平面滚动堆栈的操作可模拟组织的物理组织学切片过程。 视频3：以单切片序列遍历X轴堆栈的视频。该视频为XRH图像堆栈沿YZ平面的横截面视图。XRH数据集通常会经过方向调整（重切片），使得沿XY平面滚动堆栈的操作可模拟组织的物理组织学切片过程。 视频4：三维X射线组织学（XRH）是一种基于微计算机断层扫描（micro-computed tomography, µCT）的工作流程，可无缝适配生物医学、临床前研究以及临床组织病理学领域的现有组织学工作流程。该技术可从标准（未染色）福尔马林固定石蜡包埋（formalin-fixed and paraffin-embedded, FFPE）组织块中捕获显微解剖细节。 视频5：样本沿组织学相关平面的平均强度投影（Average Intensity Projection, AIP）可视化结果。该二维可视化效果展示了沿堆栈Z轴的20组单XY切片的平均强度值。XRH数据集通常会经过方向调整（重切片），使得沿XY平面滚动堆栈的操作可模拟组织的物理组织学切片过程。 视频6：样本沿组织学相关平面的最大强度投影（Maximum Intensity Projection, MIP）可视化结果。该二维可视化效果展示了沿堆栈Z轴的20组单XY切片的最大强度值。XRH数据集通常会经过方向调整（重切片），使得沿XY平面滚动堆栈的操作可模拟组织的物理组织学切片过程。 视频7：样本沿组织学相关平面的标准差投影可视化结果。该二维可视化效果展示了沿堆栈Z轴的20组单XY切片的标准差。XRH数据集通常会经过方向调整（重切片），使得沿XY平面滚动堆栈的操作可模拟组织的物理组织学切片过程。 * 视频5至7也可称为"厚切片卷展"——厚切片卷展是一种二维厚切片查看方式，支持沿3D数据的Z轴滚动预设数量（n）的切片。单次向前厚切片卷展可通过将厚切片向前移动一个单切片完成：即从首个及第n个切片元素向前移动一个（+1）切片，并将相应标准或操作重新应用于新的切片子堆栈。 用于收集XRH社区需求反馈的调查问卷。Survey.docx、Survey.pdf 半自动生成的增强型PDF报告示例，包含样本信息、成像设置、带描述性图注的静态图像以及对应在线视频的链接：DEMO02019-FFPE_report_99EbPXG.pdf ================================== 系统性能数据压缩包 ================================== 该压缩包包含南安普顿大学μ-VIS X射线成像中心XRH设施在不同系统及配置下采集的成像数据，用于设备验收和/或系统性能表征。以下为文件夹结构及其内容概述： 以下文件为2017年9月28日使用Med-X系统搭配JIMA体模，在峰值电压55 kV、功率7 W条件下采集的X射线成像数据： 20170928_MEDX_1642_JIMA_55kVp7W-2.tif 20170928_MEDX_1642_JIMA_55kVp7W.tif 20170928_MEDX_1642_JIMA_55kVp7W.tif.profile.xml 该PDF文档与QRM微CT条形体模相关，包含其规格说明：QRM-MicroCT-Barpattern-Phantom.pdf 展示通过边缘调制函数测试计算得到的钼旋转靶焦点尺寸随X射线功率（W）变化的图表，并将其性能与相同功率范围内的反射靶性能进行对比。原始数据可在XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize文件夹中获取。该测试于2021年7月完成：XRH_202107_MoRot-testing_EdgeModFunction-QRMrecons+RotReflCompar.png /XRH-XT-H-225-ST_FocalSpots 目录： 包含使用XRH系统搭配JIMA体模，以及钼旋转（MoRt）、透射（TT）、反射（Reflection）靶材采集的射线成像数据。 - 20200113_XRH_Jima test MoRT 55kV 15W.tif、20200113_XRH_Jima test MoRT 55kV 30W.tif等：为2020年1月13日使用XRH系统、JIMA体模、钼旋转靶，在55 kVp条件下以不同功率采集的射线照片。 - 20200207_XRH_JIMA 80kV TT1a.tif、20200207_XRH_JIMA 80kV TT1b.tif等：与上述类似，为2020年2月7日使用XRH系统、JIMA体模，在80 kVp条件下搭配透射靶采集的射线照片。 - 20231115_XRH_reflW_80kVp6W.tif、20231115_XRH_reflW_80kVp6W_02.tif等：为2023年11月15日使用XRH系统搭配反射靶，在80 kVp、6 W条件下采集的成像数据。 /XRH_QRM_Refl-vs-Rot-TargetComparison_SingleRadioFromCTs_5umPixelSize 目录： 包含使用钼旋转（MoRt）靶材以及钨（W）、钼（Mo）反射靶材，以5微米像素尺寸采集的单张射线照片。 /XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize 目录： 包含上述配置的单张重建切片。这些切片从CT体数据中导出，用于边缘调制函数研究。 针对上述文件夹内文件名的解读说明如下，请结合具体文件及文件夹获取各成像会话的详细信息与结果： - <xx>kVp 或 <xx>kV：代表峰值电压为<xx> kVp的成像参数。 - <y>W：代表成像功率为<y>瓦；小数点以"-"替代，例如20210705_XRH_2766_PJB_TEST03552-EQPMT_W_6-9W表示采用6.9 W功率采集的数据。 - MoRt, TT, Refl：分别代表钼旋转靶、透射靶与反射靶。 - _W_ 与 _Mo_：分别代表钨靶与钼靶材料。 - _horiz：代表与X射线束传播方向一致的重建切片。 - _vert：代表垂直于X射线束传播方向且平行于探测器平面的重建切片。