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

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System performance data ZIP
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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.