README file for: '3D cyclorama for digital unrolling and visualisation of deformed tubes'

Dataset DOI: 10.5258/SOTON/D1407

README Author: Charalambos Rossides, University of Southampton [ORCID: 0000-0002-7547-0256]

This dataset supports the publication:
AUTHORS: 
	Charalambos Rossides
	Sylvia L.F. Pender
	Philipp Schneider
TITLE: 3D cyclorama for digital unrolling and visualisation of deformed tubes
JOURNAL: Scientific Reports
PAPER DOI IF KNOWN: -

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 
		
Date of data collection: 2017 - 2019

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

Date that the file was created: June 2021