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

<strong>Video files and logs</strong> 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. List of files: 20211019-23h59m_20xAvgInt.mp4 20211019-23h59m_20xAvgInt.txt 20211019-23h59m_20xMaxInt.mp4 20211019-23h59m_20xMaxInt.txt 20211019-23h59m_20xStDev.mp4 20211019-23h59m_20xStDev.txt 20211019-23h59m_XYSliceRoll.mp4 20211019-23h59m_XYSliceRoll.txt 20211019-23h59m_XZSliceRoll.mp4 20211019-23h59m_XZSliceRoll.txt 20211019-23h59m_YZSliceRoll.mp4 20211019-23h59m_YZSliceRoll.txt * <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> <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). List of volume files: <strong>32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw</strong> sample: Human lung adenocarcinoma histology-relevant resliced volume (2x2x2 3D medial filter applied) import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic <strong>cBC_32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1588x1674x164x16bit.raw</strong> sample: Human lung adenocarcinoma cassette artefacts background correction (bandpass) of volume 32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic <strong>Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw</strong> sample: Human head and neck tumour histology-relevant resliced volume (1x1x1 3D medial filter applied) import as 2000 x 1952 x 501 x 32-bit, big-endian; voxel edge size (mm): 0.00999782 isotropic <strong>Conventional Histology and correlative imaging</strong> <strong>HN2_Level001_MEDX080_Manual_BW_Series4.tif</strong> H&amp;E histology slice of the human head and neck tumour sample shown in "Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw" <strong>HN2_Level001_MEDX080_Manual_BW</strong> manual landmark selection used for registering the conventional histology slice onto the μCT slice <strong>HN2_MEDX_rotated_0080.tif</strong> 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"