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

Video files and logs

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

* 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.

Volume XRH data
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:

32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw

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

cBC_32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1588x1674x164x16bit.raw

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

Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw

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

Conventional Histology and correlative imaging

HN2_Level001_MEDX080_Manual_BW_Series4.tif

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"

HN2_Level001_MEDX080_Manual_BW

manual landmark selection used for registering the conventional histology slice onto the μCT slice

HN2_MEDX_rotated_0080.tif

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"