Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 9785322

A JAVA environment for medical image data analysis: initial application for brain PET quantitation.

K Mikolajczyk·M Szabatin·P Rudnicki·M Grodzki·C Burger
View original source ↗Export metadata ↓

Abstract

Analysis software for medical image data tends to be expensive and usable only in a restricted environment. Therefore the aim of the current project was to implement a flexible framework for medical image processing and visualization which is portable among platforms and open to different data formats including DICOM 3.0. The software was designed as a set of tools which encapsulate specialized functionality. The tools are full stand alone applications, but they are also able to present a co-operating environment within which images and other information are communicated in real time. Currently, the emphasis is on quantitative analysis of PET data by kinetic modelling. However, general viewing capabilities are included, and the design is flexible enough that other types of processing can easily be integrated by simply plugging in Java classes. The software is successfully applied to PET data quantitation in clinical research studies and even patient studies. Portability was aimed at by encoding the programs in Java. Experience shows that the implementation of such a complex and computationally demanding Java application is feasible. Although there are major portability issues to consider, configurations can be found on which the software runs stably and at a speed comparable to C code if just-in-time compilation is available.

Explore related subjects

BrainHumansImage Processing, Computer-AssistedInternetProgramming LanguagesRadiology Information SystemsSoftwareTomography, Emission-ComputedJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

K Mikolajczyk, M Szabatin, P Rudnicki, M Grodzki, C Burger. A JAVA environment for medical image data analysis: initial application for brain PET quantitation.. https://doi.org/10.3109/14639239809001400

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

A MAGIBU-based model for pediatric and juvenile CNS tumors: an in-house epigenetic decision-support framework compared with online DNA methylation classifiers.

Background: DNA methylation profiling is a tool that provides key support for central nervous system (CNS) tumor classification. However, diagnostically ambiguous pediatric cases may result in discordant outputs across classifiers. We developed MAGIBU, a cross-platform, projection-based framework that embeds individual methylomes into a fixed CNS reference landscape, ranking diagnostic entities by local epigenetic proximity to support clinician-led integrative diagnosis. Methods: As a proof-of-concept, we evaluated MAGIBU in eight morphologically challenging pediatric/juvenile CNS tumors with unresolved diagnoses after institutional and central pathology review. To establish a benchmark in the absence of a definitive histopathological ground truth, a consensus epigenetic reference was defined a priori for cases showing concordant results between the Heidelberg CNS Tumor Methylation Classifier and Methylscape Analysis. Comparisons were also performed with Epigenomic Digital Pathology (EpiDiP). To validate MAGIBU beyond this discovery cohort, performance was assessed at the family level across the CNS methylation spectrum (n = 678, 28 methylation families), on non-array platforms (whole-genome bisulfite sequencing and Oxford Nanopore), and in a focused analysis of the low-grade glioma and diffuse midline glioma compartment across four independent cohorts (n = 670). Results: In the discovery cohort, MAGIBU achieved high concordance with the consensus reference (Cohen's κ = 0.855), outperforming EpiDiP (κ = 0.278), which frequently placed low-grade tumors in proximity to higher-grade reference regions. Conclusions: MAGIBU provides a stable, quantitative differential diagnosis framework that mitigates the limitations of rigid categorical assignments. By leveraging a distance-based proximity metric, it offers a transparent decision-support tool that integrates effectively with clinical, radiological, and molecular data. While performance is inherently dependent on reference atlas composition, MAGIBU represents a robust complementary approach for the diagnostic workup of ambiguous CNS tumors.

Brain↗
PubMed2021

1q21.1 distal copy number variants are associated with cerebral and cognitive alterations in humans.

Low-frequency 1q21.1 distal deletion and duplication copy number variant (CNV) carriers are predisposed to multiple neurodevelopmental disorders, including schizophrenia, autism and intellectual disability. Human carriers display a high prevalence of micro- and macrocephaly in deletion and duplication carriers, respectively. The underlying brain structural diversity remains largely unknown. We systematically called CNVs in 38 cohorts from the large-scale ENIGMA-CNV collaboration and the UK Biobank and identified 28 1q21.1 distal deletion and 22 duplication carriers and 37,088 non-carriers (48% male) derived from 15 distinct magnetic resonance imaging scanner sites. With standardized methods, we compared subcortical and cortical brain measures (all) and cognitive performance (UK Biobank only) between carrier groups also testing for mediation of brain structure on cognition. We identified positive dosage effects of copy number on intracranial volume (ICV) and total cortical surface area, with the largest effects in frontal and cingulate cortices, and negative dosage effects on caudate and hippocampal volumes. The carriers displayed distinct cognitive deficit profiles in cognitive tasks from the UK Biobank with intermediate decreases in duplication carriers and somewhat larger in deletion carriers-the latter potentially mediated by ICV or cortical surface area. These results shed light on pathobiological mechanisms of neurodevelopmental disorders, by demonstrating gene dose effect on specific brain structures and effect on cognitive function.

Brain↗
PubMed2000

A terminal deletion of the short arm of chromosome 3: karyotype 46, XY, del (3) (p25-pter); a case report and literature review.

We describe a boy with a deletion of the short arm of chromosome 3; (46, XY, del (3) (p25-pter) who presented several minor craniofacial anomalies at birth. Only 34 cases of small distal 3p deletion have been described in the literature, seven of them showed hearing loss and four of the 34 cases had brain anomalies. But in none of the 34 cases the middle and internal ear were radiographically examined. Despite the severe hearing loss detected by auditory brainstem evoked responses (ABR), computerized tomographic scanning (CT-scan) of the ear showed a normal anatomy in this patient. The head CT-scan and magnetic resonance imaging (MRI) disclosed a hypoplastic corpus callosum and an enlargement of the lateral ventricles.

Brain↗