Image Analysis Visual Tools

Imaging rating tool, protocols and repository, software tools, and radiology review tools.

Freely available, downloadable software, mostly developed locally at the University of Edinburgh

Normal Ageing Brain Rating Tools

Ageing Brain Template (129.94 KB / PDF)

Atrophy Ranking (179.47 KB / PDF)

Ageing Brain Paper (316.36 KB / PDF)

Normal Ageing Brain template (999.38 KB / PDF)

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Brain Imaging of Normal Subjects (BRAINS) software tool

Age-specific MR atlases from young adults to the very elderly (475.45 KB / PDF)

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Human brain atlases across the lifespan – Anatomical Segmentations, 1990-2016 [dataset]

https://datashare.ed.ac.uk/handle/10283/3890

Downloadable DICOM image anonymization: DICOM Confidential software tools

Anonymization of DICOM images: DICOM Confidential software tool

DICOM Confidential download | SourceForge.net

Functional MR (fMRI): adaptive thresholding software tools

Electro-encephalography (EEG) statistical analysis software tool

LIMO EEG toolbox: for statistical analysis of EEG data across the whole dataspace (EEGLAB compatible)

Robust correlation software tools

The Robust Correlation Toolbox is a free collection of MATLAB functions allowing:Visualization of data in univariate & bivariate spaceChecking assumptions of normality & homoscedasticityComputation of Pearson's & Spearman's coefficients, percentage bend & skipped correlations with bootstrapped confidence intervals

Brain observer microbleed scale (BOMBS) rating tools

Brain Observer Microbleed Scale (BOMBS) User Guide (1.85 MB / PDF)

Brain Observer Microbleed Scale (BOMBS) Form (129.52 KB / PDF)

Development of BOMBS (523.25 KB / PDF)

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Segmentation of microbleeds & mineral deposits software tool

Guidelines for segmentation of microbleeds & mineral deposits (482.92 KB / PDF)

Multi-Centre Studies

Edinburgh Imaging publication on Guidelines & Practical Tips for accurate & reproducible imaging endpoints & data sharing

Metrics for quality control of results from super-resolution machine-learning algorithms – Data extracted from publications in the period 2017- May 2021, 2017-2021 [dataset]

https://datashare.ed.ac.uk/handle/10283/3933

Enlarged Perivascular Spaces (EPVS) rating tools

Quantifying Enlarge Perivascular Spaces (EPVS) (1.53 MB / PDF)

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Digital human brain atlases software tool

https://datashare.ed.ac.uk/handle/10283/2216

Dynamic contrast enhanced magnetic resonance (DCE-MR) software tool

Patlak modelling of subtle Blood Brain Barrier (BBB) leakage

Mapping T1 (volumetric) software tool

DESPOT1-HIFI or variable flip angle

Mapping T1 software tool

Mapping T2/T2* software tool

https://github.com/mjt320/T2Star

Vascular assessment & measurement platform for images of the retina (VAMPIRE) – analysis software

Semi-automatic software to measure fundus images (fundus camera, SLO & Optos ultra-widefield SLO) are also available.
For further info, please contact:

Dr Tom MacGillivray

Senior Research Fellow & Image Analysis Core Laboratory Manager

Centre for Clinical Brain Sciences
Clinical Research Imaging Centre
Wellcome Trust Clinical Research Facility

Contact details

Website: Profile on the University of Edinburgh
Website: Profile on Edinburgh Research Explorer
Website: Clinical Research Imaging Centre Image Analysis
Work: +44 (0)131 242 7756
Email: T.J.MacGillivray@ed.ac.uk

Segmentation of brain tissue: image processing methods

ALFA - Algorithm for MRI neonatal brain extraction

MRBrainS Challenge paper

Segmentation of brain tissues & lesions software tool

A multispectral method for segmentation of brain tissues & lesions, developed for the BRIC1936 study

Segmentation of microbleeds & mineral deposits software tool

Guidelines for segmentation of microbleeds & mineral deposits (482.92 KB / PDF)

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Segmentation of mineral deposits in MR brain volumes software tool

https://github.com/aglatz/mineral-deposit-segmentation-pipeline

Tissue irregularity map software tool

https://github.com/febrianrachmadi/lots-iam-gpu

Reference segmentations software tool

https://datashare.ed.ac.uk/handle/10283/2147

Digital human brain atlases software tool

https://datashare.ed.ac.uk/handle/10283/2215

Brain imaging of normal subjects (BRAINS) software tool

https://datashare.ed.ac.uk/handle/10283/1957

Acute ischaemic stroke rating tools

Acute Stroke Lesions Proforma (37.39 KB / PDF)

CT and MR reading form (1.04 MB / PDF)

CT Perfusion and Angiography form (1.16 MB / PDF)

MRI Perfusion and Angiography studies reading form (808.18 KB / PDF)

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White matter hyperintensities evolution patterns 1 year post-lacunar stroke & their association with post-stroke cognition, 2009-2013 [dataset]

https://datashare.ed.ac.uk/handle/10283/3934

Systematic Review & Meta-Analysis on incidence & risk of stroke in individuals with long-term exposure to air pollutants, [dataset]

https://datashare.ed.ac.uk/handle/10283/3932

White matter lesion (WML) rating tools

20 MR scans with ratings (2.1 MB / PDF)

WML Rating Scales Recording Sheet (4.39 KB / PDF)

Longstreth Rating Tool (430.48 KB / PDF)

Fazekas Scale (251.85 KB / PDF)

Wahlund Rating Scale (287.57 KB / PDF)

Prins Rating Scale (49.68 KB / PDF)

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Segmentation of brain tissues & lesions software tool

A multispectral method for segmentation of brain tissues & lesions, developed for the BRIC1936 study

Tissue irregularity map software tool

https://github.com/febrianrachmadi/lots-iam-gpu

Reference segmentations software tool

https://datashare.ed.ac.uk/handle/10283/2147

Digital human brain atlases software tool

https://datashare.ed.ac.uk/handle/10283/2215

Brain imaging of normal subjects (BRAINS) software tool

https://datashare.ed.ac.uk/handle/10283/1957

Inferior Frontal Sulcal Hyperintensity (IFSH) Scale: user guide & related template

https://data.mendeley.com/datasets/wh4dgpswgc/1

White matter hyperintensities evolution patterns 1 year post-lacunar stroke & their association with post-stroke cognition, 2009-2013 [dataset]

https://datashare.ed.ac.uk/handle/10283/3934

This article was published on 2025-07-21