Three-dimensional segmentation of computed tomography data using
            <i>Drishti Paint</i>
            : new tools and developments

Hu, Yuzhi; Limaye, Ajay; Lü, Jing

doi:10.1098/rsos.201033

Cited by 28 publications

(9 citation statements)

References 43 publications

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“…Raw images from all scans were reconstructed using the FDK algorithm. Reconstructed scan data were imported into VG Studio software version 3.1(Volume Graphics, Inc., NC, USA) and Drishti Volume Exploration Software 74 for 3D rendering of bone and soft tissue.…”

Section: Methodsmentioning

confidence: 99%

FOXI3 pathogenic variants cause one form of craniofacial microsomia

et al. 2023

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Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set of abnormalities. These birth defects are associated with structures derived from the first and second pharyngeal arches, can occur unilaterally and include ear dysplasia, microtia, preauricular tags and pits, facial asymmetry and other malformations. The inheritance pattern is controversial, and the molecular etiology of this syndrome is largely unknown. A total of 670 patients belonging to unrelated pedigrees with European and Chinese ancestry with CFM, are investigated. We identify 18 likely pathogenic variants in 21 probands (3.1%) in FOXI3. Biochemical experiments on transcriptional activity and subcellular localization of the likely pathogenic FOXI3 variants, and knock-in mouse studies strongly support the involvement of FOXI3 in CFM. Our findings indicate autosomal dominant inheritance with reduced penetrance, and/or autosomal recessive inheritance. The phenotypic expression of the FOXI3 variants is variable. The penetrance of the likely pathogenic variants in the seemingly dominant form is reduced, since a considerable number of such variants in affected individuals were inherited from non-affected parents. Here we provide suggestive evidence that common variation in the FOXI3 allele in trans with the pathogenic variant could modify the phenotypic severity and accounts for the incomplete penetrance.

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Section: Methodsmentioning

confidence: 99%

FOXI3 pathogenic variants cause one form of craniofacial microsomia

et al. 2023

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“…The image stack was cropped, optimized for brightness and contrast, and saved in tif-format. The tif-stack was then imported using Drishti Import v2.7 and structures of interest (skull bones, bony labyrinth, membranous labyrinth, neuronal structures) were manually segmented in Drishti [ 9 ]. Drishti files were imported in Meshlab_64bit_fp v2021.10 [ 10 ] and rendered as 3D-models.…”

Section: Methodsmentioning

confidence: 99%

Malformations of the sacculus and the semicircular canals in spider morph pythons

Starck

Schrenk²,

Schröder

et al. 2022

PLoS ONE

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Spider morph ball pythons are a frequently-bred designer morph with striking alterations of the skin color pattern. We created high-resolution μCT-image series through the otic region of the skulls, used 3D-reconstruction software for rendering anatomical models, and compared the anatomy of the semicircular ducts, sacculus and ampullae of wildtype Python regius (ball python) with spider morph snakes. All spider morph snakes showed the wobble condition (i.e., twisting movements of the head, impaired locomotion, difficulty striking or constricting prey items). We describe the inner ear structures in wildtype and spider morph snakes and report a deviant morphology of semicircular canals, ampullae and sacculus in the latter. We also report about associated differences in the desmal skull bones of spider morph snakes, which were characterized by wider semicircular canals, ampullae widened and difficult to discern in μCT, a deformed crus communis, and a small sacculus with a highly deviant X-ray morphology as compared to wildtype individuals. We observed considerable intra- and interindividual variability of these features. This deviant morphology in spider morph snakes could easily be associated with an impairment of sense of equilibrium and the observed neurological wobble condition. Limitations in sample size prevent statistical analyses, but the anatomical evidence is strong enough to support an association between the wobble condition and a malformation of the inner ear structures. A link between artificially selected alterations in pattern and specific color design with neural-crest associated developmental malformations of the statoacoustic organ as known from other vertebrates is discussed.

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“…DRISHTI [25,26] is a visualisation tool for 3D pixel data, which has been extended with segmentation and measurement tools.…”

Section: Glossarymentioning

confidence: 99%

A Hitchhiker's guide through the bio‐image analysis software universe

et al. 2022

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Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualising information derived from microscopy imaging data of biological samples. In the past decade, we observed a dramatic increase in available software packages for these purposes. As it is increasingly difficult to keep track of the number of available image analysis platforms, tool collections, components and emerging technologies, we provide a conservative overview of software that we use in daily routine and give insights into emerging new tools. We give guidance on which aspects to consider when choosing the platform that best suits the user's needs, including aspects such as image data type, skills of the team, infrastructure and community at the institute and availability of time and budget.

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Three-dimensional segmentation of computed tomography data using Drishti Paint : new tools and developments

Cited by 28 publications

References 43 publications

FOXI3 pathogenic variants cause one form of craniofacial microsomia

FOXI3 pathogenic variants cause one form of craniofacial microsomia

Malformations of the sacculus and the semicircular canals in spider morph pythons

A Hitchhiker's guide through the bio‐image analysis software universe

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