The University of Southampton
University of Southampton Institutional Repository

3D histopathology – a lung tissue segmentation workflow for microfocus X-ray computed tomography scans

Wollatz, Lasse, Johnston, Steven, Lackie, Peter and Cox, Simon (2017) 3D histopathology – a lung tissue segmentation workflow for microfocus X-ray computed tomography scans Journal of Digital Imaging (doi:10.1007/s10278-017-9966-5).

Record type: Article


Lung histopathology is currently based on the analysis of 2D sections of tissue samples. The use of microfocus X-ray computed tomography (µCT) imaging of unstained soft tissue can provide high resolution 3D image datasets in the range of 2-10μm without affecting the current diagnostic workflow. Important details of structural features such as the tubular networks of airways and blood vessels are contained in these datasets but are difficult and time consuming to identify by manual image segmentation.
Providing 3D structures permits a better understanding of tissue functions and structural inter-relationships. It also provides a more complete picture of heterogeneous samples. In addition 3D analysis of tissue structure provides the potential for an entirely new level of quantitative measurements of this structure that have previously been based only on extrapolation from 2D sections.
In this paper a workflow for segmenting such 3D images semi-automatically has been created using and extending the ImageJ open-source software and key steps of the workflow have been integrated into a new ImageJ plug-in called LungJ.
Results indicate an improved workflow with a modular organization of steps facilitating the optimization for different sample and scan properties with expert input as required. This allows for incremental and independent optimization of algorithms leading to faster segmentation. Representations of the tubular networks in samples of human lung, building on those segmentations, have been demonstrated using this approach.

PDF 3D Histopathology – A Lung Tissue Segmentation Workflow for Microfocus X-ray Computed Tomography Scans - Accepted Manuscript
Restricted to Repository staff only until 24 March 2018.
Download (956kB)

More information

Submitted date: 16 December 2016
Accepted/In Press date: 12 March 2017
e-pub ahead of print date: 24 March 2017
Keywords: Lung, Image segmentation, computed tomography, Histopathology, ImageJ, Vascular Network
Organisations: Computational Engineering & Design Group, Clinical & Experimental Sciences, Education Hub


Local EPrints ID: 406469
ISSN: 0897-1889
PURE UUID: cf3a7d9d-25fd-454c-ac57-e148b8110ca9
ORCID for Steven Johnston: ORCID iD
ORCID for Peter Lackie: ORCID iD

Catalogue record

Date deposited: 18 Mar 2017 02:05
Last modified: 17 Jul 2017 13:57

Export record


Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton:

ePrints Soton supports OAI 2.0 with a base URL of

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.