muvis-tomography/XRH-processing-toolbox

XRH Processing Toolbox

The XRH Processing Toolbox is a collection of Fiji scripts that are designed to process micro CT datasets, specifically 3D X-ray Histology (XRH) data. XRH is a cutting-edge technology developed as part of the Wellcome-funded project, in collaboration with the University of Southampton and the University Hospital Southampton (UHS) NHS Foundation Trust. XRH involves the use of microfocused computed tomography (μCT)-based technology to create three-dimensional (3D) images of tissue specimens, allowing researchers to study tissue microstructures in their full three-dimensional context.

The XRH Processing Toolbox offers a range of features to enhance and improve the quality of XRH data, including automatic video generation, line suppression, intensity equalisation, slice boosting, background correction, and more. These scripts were developed as part of the XRH project and are aimed at helping researchers analyse and interpret their XRH data more effectively.

XRH Facility at UHS
www.xrayhistology.org
https://doi.org/10.12688/wellcomeopenres.19666.1

The XRH facility, located at the University Hospital Southampton (UHS), is a state-of-the-art facility and is a part of the μ-VIS X-ray Imaging Centre (www.muvis.org) and the university's Biomedical Imaging Unit. It supports and develops a wide range of biomedical imaging applications using XRH technology. The facility offers advanced imaging capabilities, including whole-block μCT-based X-ray histology imaging of formalin-fixed and paraffin-embedded tissue specimens, correlative imaging, data visualisation, image quantification, and more.

The XRH facility is open to national and international clients through various accessing options. 

** Note: This toolbox is intended to be used with XRH data and requires basic knowledge of Fiji/ImageJ. It is recommended to refer to the documentation and user manual for detailed instructions on using the toolbox and its scripts.

Features include:

* Automatic generation of videos from single and thick slice stacks
* Suppression of line- artefacts in XRH images
* Automatic concatenation and intensity equalisation, when stitching of multiple XRH volumes is required
* Image quality and contrast boosting using at "thick-slice-roll" method [ Experimental! ]
* Equalisation of variable background intensities between consequent slices within a XRH image stack 
* Thick slice stack generation
* Bicubic stack resizing
* Enhancement script of XRH images
* Relevant on histology-relevant planes
* and more

Usage

* Download the XRH Processing Toolbox.
* Open ImageJ and go to "Plugins" > "Macros" > "Run" to run the desired script on your XRH data.
* Follow the prompts and options provided by the script to process your XRH data.

Licence
This toolbox is released under the Apache v2.0 licence, allowing users to freely use, modify, and distribute the scripts.
For more information, contact O.Katsamenis@soton.ac.uk, xrh@soton.ac.uk or muvis-info@soton.ac.uk.

** Note: This toolbox is intended to be used in conjunction with XRH data and requires basic knowledge of ImageJ. It is recommended to refer to the documentation and user manual for more detailed instructions on using the toolbox and the individual scripts.