Under this section you will find "getting started" material and guidance for specific software that is relevant to XRH visualisation and/or analysis.
There are a number of volume visualisation and analysis software available, some of which are free and others are commercial products. A representative (but by no means exhaustive) list of tools that can be used for XRH is presented below.
Software pages (external)
Fiji/ImageJ - popular open-source image processing packages
Dragonfly - 3D Visualization and Analysis
Avizo - a powerful, multifaceted tool for visualising, manipulating, and understanding scientific and industrial data
Horos - open source medical image viewer for Mac, based on OsiriX and other open source medical imaging libraries
OsiriX - medical image visualisation and processing for Mac, dedicated to DICOM images produced by equipment
VGStudio Max - high-end software for the visualisation and analysis of CT data
ITK-SNAP - Image segmentation designed primarily for medical images
Blob3D - Designed for efficient measurement of up to thousands of discrete features
"ImageJ is a public domain Java image processing and analysis program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.5 or later virtual machine. Downloadable distributions are available for Windows, Mac OS X and Linux. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and ‘raw’. It supports ‘stacks’ (and hyperstacks), a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations."
(read all about it: here)
Download the free Fiji software from here picking the release that is appropriate to your computer system.
Dragonfly is a software platform for the intuitive inspection of multi-scale multi-modality image data. Its user-friendly experience translates into powerful quantitative findings with high-impact visuals, driven by nuanced easy-to-learn controls.
(find out more about it at: www.theobjects.com/dragonfly/)
Dragonfly is a commercial product! However ORS currently provides the ability to use the software free-of-charge for *personal academic* purposes. To do this you need to download and install the free, fully-functional 30-day evaluation of Dragonfly and after your trial period has ended, you will need to request a non-commercial license, which will allow you to continue using Dragonfly for one year. After this period you will need to request a new license to continue using the software. (Find out more about licensing here.)
The process of requesting a license requires the user to complete and submit a questionnaire about their research portfolio and send a copy/photo of their university ID.
Download Dragonfly free of charge for personal academic use here
Visualising XRH datasets using Dragonfly - Quick guide by Orestis L. Katsamenis and the XRH team
video tutorials with step-by-step instructions and seminars on Object Research Systems YouTube channel
video tutorials with step-by-step instructions of the different functionalities of Dragonfly on Dragonfly page
(X)MedCon stands for Medical Image Conversion and it is simple raw file converter, which supports amongst others: DICOM, NIfTI and Analyse. Try this if you need to convert the supplied .vol / .raw / .tif volume files to any of these formats, when that's what your workflows requires.
(find out more about it at: https://xmedcon.sourceforge.io/Main/HomePage)
Download (X)MedCon free of charge here picking the release that is appropriate to your computer system.
Export to DICOM using XMedCon - Quick guide by Orestis L. Katsamenis and the XRH team.