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Automated PDF reporting system for X-ray histology (XRH) scan data

Automated PDF reporting system for X-ray histology (XRH) scan data
Automated PDF reporting system for X-ray histology (XRH) scan data
Our X-ray histology (XRH) facility provides a micro-computed tomography (µCT) imaging service of unstained human and animal tissue samples from a wide array of diseases. These data are shared with biomedical researchers and clinicians who are often unfamiliar with this technology and its outputs. This creates the need to rapidly process and report XRH data in a comprehensive and easily accessible way, assuming no prior user knowledge of µCT.
We created a semi-automated reporting system directly linked with our custom-built XRH sample management system (XRHMS) (Fig.1). To ensure cross-platform and multi-software compatibility, the system generates a report as augmented Portable Document Format (PDF).
The first page (Fig.2) contains sample information, photographs, and QR/DM codes linking it to the corresponding XRHMS entry. Subsequent pages list imaging settings and still images with a descriptive figure legend, linked to corresponding online videos. These videos (accessible through any web-browser and available for download) scroll through the stack and help visualise the scanned sample in different ways such as orthogonal views, maximum/average intensity projections and 3D renderings. Online videos make the report easily shareable by email (reasonable file-sizes). This allows users with the link to view videos in YouTube Viewer at the highest resolution available without needing specialist software. Links to useful resources, instructions on how to acknowledge the facility and XRH contact details come next. An appendix contains any additional views not shown in the main body of the report or other data (e.g. conventional 2D histology images).
Accompanying μCT data with a PDF report brings together information about the sample, scan images and links to videos of 3D viewing modes. Such a reporting system is very valuable and not limited to the biomedical field as it can be applied to a range of different disciplines.
Micro-CT, X-ray histology (XRH), Sample scan reporting system, Data dissemination, Biomedical Research
Konstantinopoulou, Elena
Basford, Philip J.
efd8fbec-4a5f-4914-bf29-885b7f4677a7
Katsamenis, Orestis L.
8553e7c3-d860-4b7a-a883-abf6c0c4b438
Boardman, Richard
5818d677-5732-4e8a-a342-7164dbb10df1
Chatelet, David
6371fd7a-e274-4738-9ccb-3dd4dab32928
Cox, Simon
0e62aaed-24ad-4a74-b996-f606e40e5c55
Schneider, Philipp
a810f925-4808-44e4-8a4a-a51586f9d7ad
Lackie, Peter
4afbbe1a-22a6-4ceb-8cad-f3696dc43a7a
Konstantinopoulou, Elena
Basford, Philip J.
efd8fbec-4a5f-4914-bf29-885b7f4677a7
Katsamenis, Orestis L.
8553e7c3-d860-4b7a-a883-abf6c0c4b438
Boardman, Richard
5818d677-5732-4e8a-a342-7164dbb10df1
Chatelet, David
6371fd7a-e274-4738-9ccb-3dd4dab32928
Cox, Simon
0e62aaed-24ad-4a74-b996-f606e40e5c55
Schneider, Philipp
a810f925-4808-44e4-8a4a-a51586f9d7ad
Lackie, Peter
4afbbe1a-22a6-4ceb-8cad-f3696dc43a7a

Konstantinopoulou, Elena, Basford, Philip J., Katsamenis, Orestis L., Boardman, Richard, Chatelet, David, Cox, Simon, Schneider, Philipp and Lackie, Peter (2020) Automated PDF reporting system for X-ray histology (XRH) scan data. 10th Annual Tomography for Scientific Advancement (ToScA) symposium, Online, Virtual.

Record type: Conference or Workshop Item (Poster)

Abstract

Our X-ray histology (XRH) facility provides a micro-computed tomography (µCT) imaging service of unstained human and animal tissue samples from a wide array of diseases. These data are shared with biomedical researchers and clinicians who are often unfamiliar with this technology and its outputs. This creates the need to rapidly process and report XRH data in a comprehensive and easily accessible way, assuming no prior user knowledge of µCT.
We created a semi-automated reporting system directly linked with our custom-built XRH sample management system (XRHMS) (Fig.1). To ensure cross-platform and multi-software compatibility, the system generates a report as augmented Portable Document Format (PDF).
The first page (Fig.2) contains sample information, photographs, and QR/DM codes linking it to the corresponding XRHMS entry. Subsequent pages list imaging settings and still images with a descriptive figure legend, linked to corresponding online videos. These videos (accessible through any web-browser and available for download) scroll through the stack and help visualise the scanned sample in different ways such as orthogonal views, maximum/average intensity projections and 3D renderings. Online videos make the report easily shareable by email (reasonable file-sizes). This allows users with the link to view videos in YouTube Viewer at the highest resolution available without needing specialist software. Links to useful resources, instructions on how to acknowledge the facility and XRH contact details come next. An appendix contains any additional views not shown in the main body of the report or other data (e.g. conventional 2D histology images).
Accompanying μCT data with a PDF report brings together information about the sample, scan images and links to videos of 3D viewing modes. Such a reporting system is very valuable and not limited to the biomedical field as it can be applied to a range of different disciplines.

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ToScA2020_PDFreport_abstract_v.final - Author's Original
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Slideshow
ToScA2020_PDFreports_Oral_presentation_v.final
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More information

Published date: 3 September 2020
Venue - Dates: 10th Annual Tomography for Scientific Advancement (ToScA) symposium, Online, Virtual, 2020-09-03
Keywords: Micro-CT, X-ray histology (XRH), Sample scan reporting system, Data dissemination, Biomedical Research

Identifiers

Local EPrints ID: 448229
URI: http://eprints.soton.ac.uk/id/eprint/448229
PURE UUID: 0ecc20ab-6477-427a-9eeb-3bd712aa8271
ORCID for Philip J. Basford: ORCID iD orcid.org/0000-0001-6058-8270
ORCID for Orestis L. Katsamenis: ORCID iD orcid.org/0000-0003-4367-4147
ORCID for Richard Boardman: ORCID iD orcid.org/0000-0002-4008-0098
ORCID for Philipp Schneider: ORCID iD orcid.org/0000-0001-7499-3576
ORCID for Peter Lackie: ORCID iD orcid.org/0000-0001-7138-3764

Catalogue record

Date deposited: 15 Apr 2021 16:34
Last modified: 18 May 2021 01:40

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Contributors

Author: Elena Konstantinopoulou
Author: David Chatelet
Author: Simon Cox
Author: Peter Lackie ORCID iD

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