1,720,962 research outputs found
Soft tissue-optimised micro-computed tomographic imaging for the study of early stages of colorectal cancer.
No full textColorectal cancer (CRC) is the third most common cause of cancer-related deaths worldwide, where diagnosis at early stage is vital for effective treatment. We hypothesise that high-resolution 3D imaging can reveal aspects of CRC initiation and progression that are not easily perceived through 2D histology, the current gold standard for diagnosis. We employed soft tissue-optimised X-ray micro-computed tomography (µCT) to explore how the colonic structure changes during early stages of CRC. Azoxymethane and dextran sodium sulphate (AOM/DSS) were used to induce inflammation-associated CRC in 36 male C57BL/6J mice, recreating the conditions of three distinct stages of CRC: early-initiation, mid-progression and late-cancerous tumours. To increase the inherently low X-ray contrast of the colon, so-called in-line phase contrast synchrotron µCT imaging was employed. This advanced imaging technique provides increased image contrast of soft tissues, due to the coherence of the synchrotron source. Our sample preparation protocol for µCT imaging involved fixation in 10% neutral buffered formaldehyde for 24 hours and embedding in cylindrical wax blocks (5 mm diameter and height). Formalin-fixed paraffin-embedded colons of 18 controls and 18 CRC-treated mice were scanned at the I13-2 beamline of Diamond Light Source, the UK’s national synchrotron. The high spatial resolution (pixel-size was 2.2 µm), the high image contrast and the 3D results allowed for resolving the microstructural details of colonic crypts, which play a significant role in identifying changes of colonic structures during different stages of CRC. We are currently studying and identifying structural markers of early-stage CRC, with the aim to investigate how the novel high-resolution 3D µCT data can complement and improve the diagnostic information from microscopic images of conventional 2D histology slides. In the long run, our ambition is to establish the foundations for routine ‘3D X-ray histology’ using lab-based µCT for the diagnosis of soft tissue-related diseases such as CRC
3D cyclorama for digital unrolling and visualisation of deformed tubes
No full textThis 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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Detection of early-stage colorectal cancer using synchrotron phase contrast X-ray micro-computed tomography in an azoxymethane and dextran sodium sulphate murine model.
No full textPhase-contrast imaging in practice: protocol design flowchart for X-ray propagation-based phase-contrast imaging
No full textColonic cycloramas for quantification of 3D crypt morphology in mice at progressive stages of colorectal cancer.
No full textColonic cycloramas and synchrotron X-ray phase contrast micro-computed tomographic imaging employed to study colorectal cancer in a mouse model
No full text3D cyclorama for digital unrolling and visualisation of deformed tubes
No full textColonic 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 three dimensions (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
Effects of fast X-Ray cone-beam tomographic measurement on dimensional metrology
Get PDFX-ray computed tomography (XCT) is increasingly used for dimensional metrology, where it can offer accurate measurements of internal features that are not accessible with other techniques. However, XCT scanning can be relatively slow, which often prevents routine uptake for many applications. This paper explores the feasibility of improving the speed of XCT measurements whilst maintaining the quality of the dimensional measurements derived from reconstructed volumes. In particular, we compare two approaches to fast XCT acquisition, the use of fewer XCT projections as well as the use of shortened x-ray exposure times for each projection. The study shows that the additional Poisson noise produced by reducing the exposure for each projection has significantly less impact on dimensional measurements compared to the artefacts associated with strategies that take fewer projection images, leading to about half the measurement error variability. Advanced reconstruction algorithms such as the conjugate gradient least squares method or total variation constrained approaches, are shown to allow further improvements in measurement speed, though this can come at the cost of increased measurement bias (e.g. 2.8 % increase in relative error in one example) and variance (e.g. 25 % in the same example)
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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