TINA manual landmarking tool: software for the precise digitization of 3D landmarks

Schunke, Anja C.; Bromiley, Paul A.; Tautz, Diethard; Thacker, Neil A.

doi:10.1186/1742-9994-9-6

Cited by 27 publications

(27 citation statements)

References 9 publications

(3 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As described in Additional file 1, these were optimised using a data set of 8 Mus specimens of varying species (see Table 2) with expert manual annotation of 40 mandible landmarks (see Table 3). All manual annotations were performed using the TINA software [8].…”

Section: Resultsmentioning

confidence: 99%

“…However, unlike manual annotation with AMIRA, automatic annotation with TINA does not require continuous user input. Comparison between TINA and AMIRA in terms of manual annotation accuracy is provided by [8]; note that AMIRA does not provide automatic annotation. The software made extensive use of parallelisation, and so the dependence of the run time on the number of processor cores in use was also evaluated.…”

Section: Database Size and Processor Time Requirementsmentioning

confidence: 99%

“…the time taken per point per database entry, was 1.64 seconds. In [8], the time required to manually annotate 10 landmarks on the mandible in micro-CT images of three rodent specimens (Microtus, Mus and Pachyuromys) was evaluated in both TINA and AMIRA (www.vsg3d.com/amira), both by a non-expert and an expert AMIRA user. Average timings were 13s per point using AMIRA and 30s per point using TINA for the expert, and 54s per point using AMIRA and 65s per point using TINA for the non-expert, although strong training effects were observed with TINA, as would be expected of users handling unfamiliar software.…”

Section: Database Size and Processor Time Requirementsmentioning

confidence: 99%

“…The semi-automatic landmark point localisation algorithm was implemented within the TINA Geometric Morphometrics toolkit, which also includes the TINA Manual Landmarking tool [8], and algorithms that perform quantitative shape analysis with weighted covariance estimates for increased statistical efficiency [54]. This package has been made available as free and open source software (FOSS) under the GNU General Public Licence (www.gnu.org), and can be obtained via the TINA web-site (www.tina-vision.net).…”

Section: Softwarementioning

confidence: 99%

“…In [8] the authors described a software package designed to support the process of manual landmark annotation on 3D medical image volumes, with particular reference to micro-CT images. The software presents both 2D and 3D renderings of the image volume, the latter using a fast volume rendering algorithm [9,10] in order to provide the most informative view of the data possible whilst not imposing requirements for specific graphics hardware, and provides numerous functions specifically designed to accelerate the process of landmark annotation for geometric morphometrics.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Semi-automatic landmark point annotation for geometric morphometrics

et al. 2014

Self Cite

View full text Add to dashboard Cite

Background: In previous work, the authors described a software package for the digitisation of 3D landmarks for use in geometric morphometrics. In this paper, we describe extensions to this software that allow semi-automatic localisation of 3D landmarks, given a database of manually annotated training images. Multi-stage registration was applied to align image patches from the database to a query image, and the results from multiple database images were combined using an array-based voting scheme. The software automatically highlights points that have been located with low confidence, allowing manual correction.Results: Evaluation was performed on micro-CT images of rodent skulls for which two independent sets of manual landmark annotations had been performed. This allowed assessment of landmark accuracy in terms of both the distance between manual and automatic annotations, and the repeatability of manual and automatic annotation. Automatic annotation attained accuracies equivalent to those achievable through manual annotation by an expert for 87.5% of the points, with significantly higher repeatability.Conclusions: Whilst user input was required to produce the training data and in a final error correction stage, the software was capable of reducing the number of manual annotations required in a typical landmark identification process using 3D data by a factor of ten, potentially allowing much larger data sets to be annotated and thus increasing the statistical power of the results from subsequent processing e.g. Procrustes/principal component analysis. The software is freely available, under the GNU General Public Licence, from our web-site (www.tina-vision.net).

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Database Size and Processor Time Requirementsmentioning

confidence: 99%

Section: Database Size and Processor Time Requirementsmentioning

confidence: 99%

Section: Softwarementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Semi-automatic landmark point annotation for geometric morphometrics

et al. 2014

Self Cite

View full text Add to dashboard Cite

show abstract

Evolution of a complex phenotype with biphasic ontogeny: Contribution of development versus function and climatic variation to skull modularity in toads

Simon¹,

Marroig²

2017

Ecology and Evolution

View full text Add to dashboard Cite

The theory of morphological integration and modularity predicts that if functional correlations among traits are relevant to mean population fitness, the genetic basis of development will be molded by stabilizing selection to match functional patterns. Yet, how much functional interactions actually shape the fitness landscape is still an open question. We used the anuran skull as a model of a complex phenotype for which we can separate developmental and functional modularity. We hypothesized that functional modularity associated to functional demands of the adult skull would overcome developmental modularity associated to bone origin at the larval phase because metamorphosis would erase the developmental signal. We tested this hypothesis in toad species of the Rhinella granulosa complex using species phenotypic correlation pattern (P‐matrices). Given that the toad species are distributed in very distinct habitats and the skull has important functions related to climatic conditions, we also hypothesized that differences in skull trait covariance pattern are associated to differences in climatic variables among species. Functional and hormonal‐regulated modules are more conspicuous than developmental modules only when size variation is retained on species P‐matrices. Without size variation, there is a clear modularity signal of developmental units, but most species have the functional model as the best supported by empirical data without allometric size variation. Closely related toad species have more similar climatic niches and P‐matrices than distantly related species, suggesting phylogenetic niche conservatism. We infer that the modularity signal due to embryonic origin of bones, which happens early in ontogeny, is blurred by the process of growth that occurs later in ontogeny. We suggest that the species differing in the preferred modularity model have different demands on the orbital functional unit and that species contrasting in climate are subjected to divergent patterns of natural selection associated to neurocranial allometry and T3 hormone regulation.

show abstract

Working as a Health AI Specialist

Davies

Wilson³

et al. 2021

The Health Information Workforce

View full text Add to dashboard Cite

TINA manual landmarking tool: software for the precise digitization of 3D landmarks

Cited by 27 publications

References 9 publications

Semi-automatic landmark point annotation for geometric morphometrics

Semi-automatic landmark point annotation for geometric morphometrics

Evolution of a complex phenotype with biphasic ontogeny: Contribution of development versus function and climatic variation to skull modularity in toads

Working as a Health AI Specialist

Contact Info

Product

Resources

About