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6 results for “3D X-ray Histology”
A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications - Supplementary Data
<p><strong>Videos</strong></p><ul><li><strong>Video 1</strong> 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.</li><li><strong>Video 2 </strong>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.</li><li><strong>Video 3 </strong>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.</li><li><strong>Video 4 </strong>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.</li><li><strong>Video 5</strong> 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.</li><li><strong>Video 6 </strong>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.</li><li><strong>Video 7 </strong>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.</li></ul><p><i>* <strong>Videos 5 -7</strong> are also referred to as "thick-slice rolls" </i>- <i>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.</i><br> </p><p><strong>The questionnaire used to collect feedback about the needs of the XRH community.</strong></p><ul><li>Survey.docx</li><li>Survey.pdf</li></ul><p><br><strong>Exemplar report of a semi-automatically generated augmented PDF file</strong> that contain sample information, imaging settings, still images with descriptive figure legends, and links to corresponding online videos</p><ul><li>DEMO02019-FFPE_report_99EbPXG.pdf</li></ul><p> </p><p>= = = = = = = = = = = = = = = = <br><strong>System performance data ZIP</strong><br>= = = = = = = = = = = = = = = = </p><p>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</p><p>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. </p><ul><li>20170928_MEDX_1642_JIMA_55kVp7W-2.tif</li><li>20170928_MEDX_1642_JIMA_55kVp7W.tif</li><li>20170928_MEDX_1642_JIMA_55kVp7W.tif.profile.xml</li></ul><p>This PDF document is related to a QRM MicroCT bar pattern phantom, and its specifications</p><ul><li>QRM-MicroCT-Barpattern-Phantom.pdf</li></ul><p>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. </p><ul><li>XRH_202107_MoRot-testing_EdgeModFunction-QRMrecons+RotReflCompar.png</li></ul><p> </p><p><i><strong>/ XRH-XT-H-225-ST_FocalSpots</strong></i><br>This directory contains radiographic data collected using the XRH system with a JIMA phantom and MoRt (Molybdenum rotating), TT (Transmission), and Reflection targets.</p><ul><li>20200113_XRH_Jima test MoRT 55kV 15W.tif, 20200113_XRH_Jima test MoRT 55kV 30W.tif, etc.: <br>These files represent radiographs taken on January 13, 2020, using the XRH system, Jima phantom, MoRT target at 55 kVp and varying wattages.</li><li>20200207_XRH_JIMA 80kV TT1a.tif, 20200207_XRH_JIMA 80kV TT1b.tif, etc.<br>Similar to the above, these files are from February 7, 2020, and use 80 kVp with a TT target.</li><li>20231115_XRH_reflW_80kVp6W.tif, 20231115_XRH_reflW_80kVp6W_02.tif, etc.<br>These files are from November 15, 2023, and collected using the XRH system with a Reflection target at 80 kVp and 6 Watts.</li></ul><p><i><strong>/ XRH_QRM_Refl-vs-Rot-TargetComparison_SingleRadioFromCTs_5umPixelSize</strong></i><br>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.</p><p><i><strong>/ XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize</strong></i><br>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. </p><p>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:</p><ul><li><i><xx>kVp or <xx>kV </i>:Imaging at a peak voltage of <xx> kVp.</li><li><i><y>W</i> :Imaging at <y> Watts;<i> </i>"." is represented with "-"; i.e. 20210705_XRH_2766_PJB_TEST03552-EQPMT_W_6-9W is acquired using a power of 6.9 W</li><li><i>MoRt, TT, Refl </i> :Molybdenum, Transmission, and Reflection targets, respectively.</li><li><i>_W_ and _Mo_ </i> :Tungsten and Molybdenum target materials.</li><li><i>_horiz</i> :Reconstruction slices in line with the X-ray beam's propagation direction.</li><li><i>_vert</i> :Reconstruction slices normal to the X-ray beam's propagation direction and parallel to the detector plane.</li></ul>
A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications - Underlying Data
<p><strong>Video files and logs</strong></p> <p>Single-slice and thick-slice roll* source videos are included. Each video is accompanied by a .txt log that contains information about the source file, slice thickness, and a brief description of the visualization mode.</p> <p>List of files:</p> <ul> <li>20211019-23h59m_20xAvgInt.mp4</li> <li>20211019-23h59m_20xAvgInt.txt</li> <li>20211019-23h59m_20xMaxInt.mp4</li> <li>20211019-23h59m_20xMaxInt.txt</li> <li>20211019-23h59m_20xStDev.mp4</li> <li>20211019-23h59m_20xStDev.txt</li> <li>20211019-23h59m_XYSliceRoll.mp4</li> <li>20211019-23h59m_XYSliceRoll.txt</li> <li>20211019-23h59m_XZSliceRoll.mp4</li> <li>20211019-23h59m_XZSliceRoll.txt</li> <li>20211019-23h59m_YZSliceRoll.mp4</li> <li>20211019-23h59m_YZSliceRoll.txt</li> </ul> <p>* <em>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.</em></p> <p><strong>Volume XRH data</strong><br> These are processed raw volume file saved in .raw and/or .tiff format, which are resliced to a histology-relevant orientation and/or have been enhanced using noise reduction (3D median filter) and/or ct-artefact removal techniques (e.g. cBC identifies a bandpass filter used to remove intensity variations originating from the histology cassette).</p> <p>List of volume files:</p> <ul> <li><strong>32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw</strong> <ul> <li>sample: Human lung adenocarcinoma</li> <li>histology-relevant resliced volume (2x2x2 3D medial filter applied)</li> <li>import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic</li> </ul> </li> <li><strong>cBC_32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1588x1674x164x16bit.raw</strong> <ul> <li>sample: Human lung adenocarcinoma</li> <li>cassette artefacts background correction (bandpass) of volume 32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw</li> <li>import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic</li> </ul> </li> <li><strong>Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw</strong> <ul> <li>sample: Human head and neck tumour</li> <li>histology-relevant resliced volume (1x1x1 3D medial filter applied)</li> <li>import as 2000 x 1952 x 501 x 32-bit, big-endian; voxel edge size (mm): 0.00999782 isotropic</li> </ul> </li> </ul> <p><strong>Conventional Histology and correlative imaging</strong></p> <ul> <li><strong>HN2_Level001_MEDX080_Manual_BW_Series4.tif</strong> <ul> <li>H&E histology slice of the human head and neck tumour sample shown in "Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw"</li> </ul> </li> <li><strong>HN2_Level001_MEDX080_Manual_BW</strong> <ul> <li>manual landmark selection used for registering the conventional histology slice onto the μCT slice</li> </ul> </li> <li><strong>HN2_MEDX_rotated_0080.tif</strong> <ul> <li>Slice 80 from volume "Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw" that corresponds to histological slice "HN2_Level001_MEDX080_Manual_BW"</li> </ul> </li> </ul>
3d Virtual Patho-Histology of Lung Tissue from Covid19 Patients based on Phase Contrast X-ray Tomography
<p>X-ray phase contrast tomographys datasets of lung tissue from 6 Covid-19 patients (paraffin embedded unstained tissue), and one control tissue (healthy lung, in fixative solution). The data has been recorded as part of the Covid-19 Call for Proposals at DESY April 2020 at the GINIX instrument, beamline P10 of the PETRAIII storage ring at 8keV. Three different datasets are included in a single tar archive for each sample: (i) overview scan (up to 4mm cross section ) from stitching different tomograms, (ii) 1mm cylindrical punch, and (iii) cone-beam zoom tomogram recorded with waveguide illumination. </p> <p>voxel sizes: (i) 1.3µm, (ii) 650nm, (iii) 167nm. </p> <p>3 datasets per sample, raw format, voxel numbers given in Filename, single (32bit real)</p> <p> </p>
Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Using micro-CT optimized for cellular characterization (histo-tomography), brain nuclei can be computationally segmented and assigned to brain regions. Shape and volume can be computed for populations of nuclei, motor neurons and red blood cells. Computed cell density revealed striking individual phenotypic variation. Unlike histology, histo-tomography allows the detection of phenotypes that require millimeter scale context in multiple planes. We expect the computational and visual insights into 3D tissue architecture provided by histo-tomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Open the record for dataset details and reuse information.
Tomographic datasets for '3d virtual histology of human cerebellum by x-ray phase-contrast tomography'
<p>Tomographic datasets for '3d virtual histology of human cerebellum by x-ray phase-contrast tomography' by M. Töpperwien et al. (PNAS 2018). Reconstructed volumes of both the measurements at the GINIX endstation at PETRAIII (DESY@Hamburg) and the laboratory setup are given. The datasets are saved as .raw in single-precision floating-point format and the size of each dataset is indicated in the filename. Note that in both cases the datasets are those used for the automatic segmentation via the Spherical Hough transform, meaning that for the GINIX dataset the volume was resampled by a factor of 2 and the individual slices were subsequently filtered with a Gaussian with a standard deviation of 0.3 pixels whereas for the laboratory data, the volume was reconstructed at full resolution, followed by a lowpass filtering step.</p> <p>Additionally, the output of the segmentation workflow is given as .dat files, specifying the determined cell positions and radii for both datasets.</p>
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