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

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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Identifiers

ORCID for Elena Konstantinopoulou: orcid.org/0000-0003-4077-9648

ORCID for Philip J. Basford: orcid.org/0000-0001-6058-8270

ORCID for Orestis L. Katsamenis: orcid.org/0000-0003-4367-4147

ORCID for Richard Boardman: orcid.org/0000-0002-4008-0098

ORCID for Philipp Schneider: orcid.org/0000-0001-7499-3576

ORCID for Peter Lackie: orcid.org/0000-0001-7138-3764

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