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A sample and data management system for µCT-based X-ray histology

A sample and data management system for µCT-based X-ray histology
A sample and data management system for µCT-based X-ray histology
While setting up a facility for X-ray histology (XRH) [1] in Southampton the challenge arose of how to manage samples, data and associated metadata. This is challenging as the same sample can be analysed multiple times in different states and different modalities including micro-computed tomography (μCT), conventional (2D) thin section-based histology/whole-slide imaging or immunohistochemistry. A fresh piece of tissue may be imaged, frozen, imaged, embedded in paraffin wax, imaged, and sectioned and processed using histological techniques, all of which needs to be included attached in the sample record. Moreover, sample and data management system needed to be user-friendly. These requirements have led to the development of XRHMS, a management system to keep track of all samples within the facility, their data and their metadata, as summarised in Figure 1. Metadata of interest about the sample includes details about the tissue type and origin, preparation, storage requirements and current location.

Figure 1 Information included in XRHMS
The combination of storing raw / processed image data and metadata requires careful architectural decisions, and is built on previous work in this area [2] and uses a database for the metadata and file system for the µCT data. The system can store data from multiple different acquisition systems and digitised histological slides, and is designed to be easily extensible. The XRHMS provides full tracking and accounting of all samples/data/processes and enables cross-linking between related datasets.
The XRHMS also forms the basis for automation of data processing, with preview images and slices generated automatically, as well as performing basic pre-processing, with additional features planned. The system can generate summary reports about the samples containing information about the scans performed and related images. These provide a useful overview of the scan and data interpretation guidance for people not familiar with the technique or viewing 3D datasets.
Basford, Philip J
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Konstantinopoulou, Elena
Katsamenis, Orestis L.
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Boardman, Richard
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Schneider, Philipp
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Lackie, Peter
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Cox, Simon
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Basford, Philip J
efd8fbec-4a5f-4914-bf29-885b7f4677a7
Konstantinopoulou, Elena
Katsamenis, Orestis L.
8553e7c3-d860-4b7a-a883-abf6c0c4b438
Boardman, Richard
5818d677-5732-4e8a-a342-7164dbb10df1
Schneider, Philipp
a810f925-4808-44e4-8a4a-a51586f9d7ad
Lackie, Peter
4afbbe1a-22a6-4ceb-8cad-f3696dc43a7a
Cox, Simon
0e62aaed-24ad-4a74-b996-f606e40e5c55

Basford, Philip J, Konstantinopoulou, Elena, Katsamenis, Orestis L., Boardman, Richard, Schneider, Philipp, Lackie, Peter and Cox, Simon (2020) A sample and data management system for µCT-based X-ray histology. Tomography for Scientific Advancement - 10th Edition, Online.

Record type: Conference or Workshop Item (Poster)

Abstract

While setting up a facility for X-ray histology (XRH) [1] in Southampton the challenge arose of how to manage samples, data and associated metadata. This is challenging as the same sample can be analysed multiple times in different states and different modalities including micro-computed tomography (μCT), conventional (2D) thin section-based histology/whole-slide imaging or immunohistochemistry. A fresh piece of tissue may be imaged, frozen, imaged, embedded in paraffin wax, imaged, and sectioned and processed using histological techniques, all of which needs to be included attached in the sample record. Moreover, sample and data management system needed to be user-friendly. These requirements have led to the development of XRHMS, a management system to keep track of all samples within the facility, their data and their metadata, as summarised in Figure 1. Metadata of interest about the sample includes details about the tissue type and origin, preparation, storage requirements and current location.

Figure 1 Information included in XRHMS
The combination of storing raw / processed image data and metadata requires careful architectural decisions, and is built on previous work in this area [2] and uses a database for the metadata and file system for the µCT data. The system can store data from multiple different acquisition systems and digitised histological slides, and is designed to be easily extensible. The XRHMS provides full tracking and accounting of all samples/data/processes and enables cross-linking between related datasets.
The XRHMS also forms the basis for automation of data processing, with preview images and slices generated automatically, as well as performing basic pre-processing, with additional features planned. The system can generate summary reports about the samples containing information about the scans performed and related images. These provide a useful overview of the scan and data interpretation guidance for people not familiar with the technique or viewing 3D datasets.

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tosca2020-xrhms - Accepted Manuscript
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More information

Published date: 3 September 2020
Venue - Dates: Tomography for Scientific Advancement - 10th Edition, Online, 2020-09-03

Identifiers

Local EPrints ID: 448103
URI: http://eprints.soton.ac.uk/id/eprint/448103
PURE UUID: b06a26a8-b78f-45aa-9406-c3b0784a6206
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: 01 Apr 2021 15:59
Last modified: 22 Nov 2021 03:06

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Contributors

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

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