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3D cyclorama for digital unrolling and visualisation of deformed tubes

3D cyclorama for digital unrolling and visualisation of deformed tubes
3D cyclorama for digital unrolling and visualisation of deformed tubes
This dataset supports the publication: TITLE: 3D cyclorama for digital unrolling and visualisation of deformed tubes JOURNAL: Scientific Reports PAPER DOI: https://doi.org/10.1038/s41598-021-93184-x ABSTRACT: Colonic crypts are tubular glands that multiply through a symmetric branching process called crypt fission. During the early stages of colorectal cancer, the normal fission process is disturbed, leading to asymmetrical branching or budding. The challenging shapes of the budding crypts make it difficult to prepare paraffin sections for conventional histology, resulting in colonic cross sections with crypts that are only partially visible. To study crypt budding in situ and in 3D, we employ X-ray micro-computed tomography to image intact colons, and a new method we developed (3D cyclorama) to digitally unroll them. Here, we present, verify and validate our ‘3D cyclorama’ method that digitally unrolls deformed tubes of non-uniform thickness. It employs principles from electrostatics to reform the tube into a series of onion-like surfaces, which are mapped onto planar panoramic views. This enables the study of features extending over several layers of the tube’s depth, demonstrated here by two case studies: (i) microvilli in the human placenta and (ii) 3D-printed adhesive films for drug delivery. Our 3D cyclorama method can provide novel insights into a wide spectrum of applications where digital unrolling or flattening is necessary, including long bones, teeth roots and ancient scrolls. This dataset contains: Figures of the main manuscript: Figures_main_manuscript.zip - Figure 1: Colonic histology - Figure 2: Generation of 3D cycloramas through electrostatic fields - Figure 3: Linear mapping of 3D re-slicing surfaces - Figure 4: 3D cycloramas for the study of murine colons - Figure 5: Budding crypt identification and 3D segmentation Figures of the supplementary document: Figures_supplementary.zip - Figure S1: 2D grid template and slices of the 3D cyclorama after unrolling of the digital phantom - Figure S2: Cross sections of the 3D digital phantom - Figure S3: Mathematical description of the 3D digital phantom - Figure S4: Verification of the cyclorama method using a digital 3D phantom - Figure S5: 3D cyclorama to segment placental microvilli - Figure S6: 3D cyclorama to unroll a pharmaceutical film Supporting videos: video_1_99128_201901251137_Cyclorama_Side_200to500_idx_cropped.avi video_2_99164_201906121810_Cyclorama_Side_30to330_idx_cropped_8bit.avi video_3_201903051259_Cyclorama_Side_1to901_idx_cropped.avi * The moving frames of the supporting videos are sequential slices of 3D cycloramas. The file naming is as follows: video_<no>_<ScanID>_<CycloramaTimestamp>_Cyclorama_Side_<CTdataSliceRange>_....avi where: ScanID - The unique identifier of the synchrotron micro-CT dataset. CycloramaTimestamp - A unique identifier of the 3D cyclorama file arranged as <year><month><day><time>. CTdataSliceRange - The slices of the micro-CT dataset that are contained (in the vertical dimension) of the 3D cyclorama. Supporting micro-CT datasets (2-part zip files): treated_99115 untreated_99128 * Image files within these directories can be opened with Fiji/Imagej * Directories with images that are named sequential numbers can be opened using the File>import>image sequence menu in Fiji/Imagej * 3D cycloramas (single-file image stacks) can be opened with the File>open menu in Fiji/Imagej Information about the geographic location of data collection: animal model and sample preparation were performed at the Biomedical Research Facility (BRF) and at the Histochemistry Research Unit (BRU), respectively, which are located at the Southampton General Hospital (HRU). micro-CT data were collected at beamline I13-2, Diamond Light Source, Didcot, UK Licence: CC-BY Related projects: PhD project: "Development of 3D X-ray phase-contrast Imaging and Analysis Tools for Tubular and Branching Structures with Applications in Colorectal Cancer Research" - Charalambos Rossides
University of Southampton
Rossides, Harry
8ea65ff8-3ba0-46d3-9f88-18553aedfb7d
Schneider, Philipp
a810f925-4808-44e4-8a4a-a51586f9d7ad
Pender, Sylvia
62528b03-ec42-41bb-80fe-48454c2c5242
Rossides, Harry
8ea65ff8-3ba0-46d3-9f88-18553aedfb7d
Schneider, Philipp
a810f925-4808-44e4-8a4a-a51586f9d7ad
Pender, Sylvia
62528b03-ec42-41bb-80fe-48454c2c5242

Rossides, Harry (2021) 3D cyclorama for digital unrolling and visualisation of deformed tubes. University of Southampton doi:10.5258/SOTON/D1407 [Dataset]

Record type: Dataset

Abstract

This dataset supports the publication: TITLE: 3D cyclorama for digital unrolling and visualisation of deformed tubes JOURNAL: Scientific Reports PAPER DOI: https://doi.org/10.1038/s41598-021-93184-x ABSTRACT: Colonic crypts are tubular glands that multiply through a symmetric branching process called crypt fission. During the early stages of colorectal cancer, the normal fission process is disturbed, leading to asymmetrical branching or budding. The challenging shapes of the budding crypts make it difficult to prepare paraffin sections for conventional histology, resulting in colonic cross sections with crypts that are only partially visible. To study crypt budding in situ and in 3D, we employ X-ray micro-computed tomography to image intact colons, and a new method we developed (3D cyclorama) to digitally unroll them. Here, we present, verify and validate our ‘3D cyclorama’ method that digitally unrolls deformed tubes of non-uniform thickness. It employs principles from electrostatics to reform the tube into a series of onion-like surfaces, which are mapped onto planar panoramic views. This enables the study of features extending over several layers of the tube’s depth, demonstrated here by two case studies: (i) microvilli in the human placenta and (ii) 3D-printed adhesive films for drug delivery. Our 3D cyclorama method can provide novel insights into a wide spectrum of applications where digital unrolling or flattening is necessary, including long bones, teeth roots and ancient scrolls. This dataset contains: Figures of the main manuscript: Figures_main_manuscript.zip - Figure 1: Colonic histology - Figure 2: Generation of 3D cycloramas through electrostatic fields - Figure 3: Linear mapping of 3D re-slicing surfaces - Figure 4: 3D cycloramas for the study of murine colons - Figure 5: Budding crypt identification and 3D segmentation Figures of the supplementary document: Figures_supplementary.zip - Figure S1: 2D grid template and slices of the 3D cyclorama after unrolling of the digital phantom - Figure S2: Cross sections of the 3D digital phantom - Figure S3: Mathematical description of the 3D digital phantom - Figure S4: Verification of the cyclorama method using a digital 3D phantom - Figure S5: 3D cyclorama to segment placental microvilli - Figure S6: 3D cyclorama to unroll a pharmaceutical film Supporting videos: video_1_99128_201901251137_Cyclorama_Side_200to500_idx_cropped.avi video_2_99164_201906121810_Cyclorama_Side_30to330_idx_cropped_8bit.avi video_3_201903051259_Cyclorama_Side_1to901_idx_cropped.avi * The moving frames of the supporting videos are sequential slices of 3D cycloramas. The file naming is as follows: video_<no>_<ScanID>_<CycloramaTimestamp>_Cyclorama_Side_<CTdataSliceRange>_....avi where: ScanID - The unique identifier of the synchrotron micro-CT dataset. CycloramaTimestamp - A unique identifier of the 3D cyclorama file arranged as <year><month><day><time>. CTdataSliceRange - The slices of the micro-CT dataset that are contained (in the vertical dimension) of the 3D cyclorama. Supporting micro-CT datasets (2-part zip files): treated_99115 untreated_99128 * Image files within these directories can be opened with Fiji/Imagej * Directories with images that are named sequential numbers can be opened using the File>import>image sequence menu in Fiji/Imagej * 3D cycloramas (single-file image stacks) can be opened with the File>open menu in Fiji/Imagej Information about the geographic location of data collection: animal model and sample preparation were performed at the Biomedical Research Facility (BRF) and at the Histochemistry Research Unit (BRU), respectively, which are located at the Southampton General Hospital (HRU). micro-CT data were collected at beamline I13-2, Diamond Light Source, Didcot, UK Licence: CC-BY Related projects: PhD project: "Development of 3D X-ray phase-contrast Imaging and Analysis Tools for Tubular and Branching Structures with Applications in Colorectal Cancer Research" - Charalambos Rossides

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video_1_99128_201901251137_Cyclorama_Side_200to500_idx_cropped.avi - Audiovisual
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video_2_99164_201906121810_Cyclorama_Side_30to330_idx_cropped_8bit.avi - Audiovisual
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video_3_201903051259_Cyclorama_Side_1to901_idx_cropped.avi - Audiovisual
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Published date: 2021

Identifiers

Local EPrints ID: 450336
URI: http://eprints.soton.ac.uk/id/eprint/450336
PURE UUID: f1bfb2bc-7722-4811-9d2e-f127bac17af3
ORCID for Harry Rossides: ORCID iD orcid.org/0000-0002-7547-0256
ORCID for Philipp Schneider: ORCID iD orcid.org/0000-0001-7499-3576
ORCID for Sylvia Pender: ORCID iD orcid.org/0000-0001-6332-0333

Catalogue record

Date deposited: 23 Jul 2021 17:28
Last modified: 24 Jul 2021 01:51

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Contributors

Creator: Harry Rossides ORCID iD
Research team head: Philipp Schneider ORCID iD
Research team head: Sylvia Pender ORCID iD

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