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3D cyclorama for digital unrolling and visualisation of deformed tubes.

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 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.

SUBMITTER: Rossides C

PROVIDER: S-EPMC8289852 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Visualisation of BioPAX Networks using BioLayout Express (3D).

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| S-EPMC4406191 | biostudies-literature

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| S-EPMC6199797 | biostudies-literature

MetaLook: a 3D visualisation software for marine ecological genomics.

Project description:BACKGROUND: Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenomes of environmental relevance must take into account the corresponding habitat (contextual) data, e.g. water depth, physical and chemical parameters. The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis. RESULTS: We implemented the MetaLook software for visualisation and analysis of marine ecological genomic and metagenomic data with respect to habitat parameters. MetaLook offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a centralised georeferenced database. The user can define environmental containers to organise the sequences according to different habitat criteria. To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported sequences, using the BLAST algorithm. This allows an interactive assessment of the distribution of gene functions in the environment. CONCLUSION: MetaLook allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. This software is a step towards the creation of specialised tools to study constrained distributions and habitat specificity of genes correlated with specific processes. MetaLook is available at: http://www.megx.net/metalook.

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| S-EPMC5493684 | biostudies-other

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3D visualisation of hepatitis B vaccine in the oral delivery vehicle SBA-15.

Project description:Developing a technology that enables oral vaccines to work efficiently remains a considerable effort since a number of difficulties must be addressed. The key objective being to ensure the safe passage through the harsh conditions within the gastrointestinal tract, promoting delivery that induces enhanced immune response. In the particular case of hepatitis B, the oral formulation in the nanostructured silica SBA-15 is a viable approach. As a result of its porous structure, low toxicity and structural stability, SBA-15 is capable to protect and release the hepatitis B surface antigen (HBsAg), used in the vaccination scheme, at the desired destination. Furthermore, when compared to the currently used injection based delivery method, better or similar antibody response has been observed. However, information about the organisation of the antigen protein remains unknown. For instance, HBsAg is too large to enter the 10 nm ordered mesopores of SBA-15 and has a tendency to agglomerate when protected by the delivery system. Here we report on the pH dependence of HBsAg aggregation in saline solution investigated using small angle X-rays scattering that resulted in an optimisation of the encapsulation conditions. Additionally, X-ray microscopy combined with neutron and X-ray tomography provided full 3D information of the HBsAg clustering (i.e. agglomeration) inside the SBA-15 macropores. This method enables the visualisation of the organisation of the antigen in the interior of the delivery system, where agglomerated HBsAg coexists with its immunological effective uniformly distributed counterpart. This new approach, to be taken into account while preparing the formulation, can greatly help in the understanding of clinical studies and advance new formulations.

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| PRJEB39393 | ENA

GNPS 3D WinCF Tubes

Project description:A collection of cultured microbial communities from cystic fibrosis sputum samples sectioned through an oxygen gradient and treated with antibiotics.

2016-12-14 | MSV000080397 | GNPS

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| S-EPMC3898923 | biostudies-literature

Meeting radiation therapy patients informational needs through educational videos augmented by 3D visualisation software.

Project description:IntroductionMisconceptions and uncertainties about radiotherapy compound the anxiety patients experience at the commencement of treatment. This project investigated the utility of locally produced treatment process videos in meeting patients' informational needs.MethodsIn-house video production was conducted on a voluntary basis by staff and patients at a regional Australian radiotherapy centre. Videos included real footage and animated sections created with PEARLTM 3D visualisation software (Vertual Ltd, UK) to meet specific key content objectives. Quantitative cross sectional analysis was conducted. Patients attending for simulation watched a relevant video. After their first fraction of radiotherapy they were asked to complete an ethics-reviewed questionnaire about how well the video addressed their information needs.ResultsThe survey completion rate was 29% (n = 61/212). Surveys were collected over 9 months from August 2014 to April 2015. Statistical analysis found 98% of patients reported that the video was useful in meeting one or more of the learning objectives. Forty-nine percent of patients also reported a reduction in fear and anxiety as a result of watching the video. Patients reported subsequent review of videos at home (39%), primarily to explain treatment processes to loved ones (46%).ConclusionThe combination of real footage and 3D visualisation software assisted in meeting learning objectives regarding the treatment process. Standardised videos provided consistency of information provision to patients and facilitated multiple viewings of the video if desired.

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