323 research outputs found
The natverse, a versatile toolbox for combining and analysing neuroanatomical data.
To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation and clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison across many neurons of morphology and connectivity after imaging or co-registration within a common template space. The natverse also enables transformations between different template spaces and imaging modalities. We demonstrate tools that integrate the vast majority of Drosophila neuroanatomical light microscopy and electron microscopy connectomic datasets. The natverse is an easy-to-use environment for neuroscientists to solve complex, large-scale analysis challenges as well as an open platform to create new code and packages to share with the community
The Morphological Identity of Insect Dendrites
Dendrite morphology, a neuron's anatomical fingerprint, is a
neuroscientist's asset in unveiling organizational principles in the
brain. However, the genetic program encoding the morphological identity of a
single dendrite remains a mystery. In order to obtain a formal understanding of
dendritic branching, we studied distributions of morphological parameters in a
group of four individually identifiable neurons of the fly visual system. We
found that parameters relating to the branching topology were similar throughout
all cells. Only parameters relating to the area covered by the dendrite were
cell type specific. With these areas, artificial dendrites were grown based on
optimization principles minimizing the amount of wiring and maximizing synaptic
democracy. Although the same branching rule was used for all cells, this yielded
dendritic structures virtually indistinguishable from their real counterparts.
From these principles we derived a fully-automated model-based neuron
reconstruction procedure validating the artificial branching rule. In
conclusion, we suggest that the genetic program implementing neuronal branching
could be constant in all cells whereas the one responsible for the dendrite
spanning field should be cell specific
3D CNN methods in biomedical image segmentation
A definite trend in Biomedical Imaging is the one towards the integration of increasingly complex interpretative layers to the pure data acquisition process. One of the most interesting and looked-forward goals in the field is the automatic segmentation of objects of interest in extensive acquisition data, target that would allow Biomedical Imaging to look beyond its use as a purely assistive tool to become a cornerstone in ambitious large-scale challenges like the extensive quantitative study of the Human Brain.
In 2019 Convolutional Neural Networks represent the state of the art in Biomedical Image segmentation and scientific interests from a variety of fields, spacing from automotive to natural resource exploration, converge to their development. While most of the applications of CNNs are focused on single-image segmentation, biomedical image data -being it MRI, CT-scans, Microscopy, etc- often benefits from three-dimensional volumetric expression.
This work explores a reformulation of the CNN segmentation problem that is native to the 3D nature of the data, with particular interest to the applications to Fluorescence Microscopy volumetric data produced at the European Laboratories for Nonlinear Spectroscopy in the context of two different large international human brain study projects: the Human Brain Project and the White House BRAIN Initiative
Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates
The study of cerebral anatomy in developing neonates is of great importance for
the understanding of brain development during the early period of life. This
dissertation therefore focuses on three challenges in the modelling of cerebral
anatomy in neonates during brain development. The methods that have been
developed all use Magnetic Resonance Images (MRI) as source data.
To facilitate study of vascular development in the neonatal period, a set of image
analysis algorithms are developed to automatically extract and model cerebral
vessel trees. The whole process consists of cerebral vessel tracking from
automatically placed seed points, vessel tree generation, and vasculature
registration and matching. These algorithms have been tested on clinical Time-of-
Flight (TOF) MR angiographic datasets.
To facilitate study of the neonatal cortex a complete cerebral cortex segmentation
and reconstruction pipeline has been developed. Segmentation of the neonatal
cortex is not effectively done by existing algorithms designed for the adult brain
because the contrast between grey and white matter is reversed. This causes pixels
containing tissue mixtures to be incorrectly labelled by conventional methods. The
neonatal cortical segmentation method that has been developed is based on a novel
expectation-maximization (EM) method with explicit correction for mislabelled
partial volume voxels. Based on the resulting cortical segmentation, an implicit
surface evolution technique is adopted for the reconstruction of the cortex in
neonates. The performance of the method is investigated by performing a detailed
landmark study.
To facilitate study of cortical development, a cortical surface registration algorithm
for aligning the cortical surface is developed. The method first inflates extracted
cortical surfaces and then performs a non-rigid surface registration using free-form
deformations (FFDs) to remove residual alignment. Validation experiments using
data labelled by an expert observer demonstrate that the method can capture local
changes and follow the growth of specific sulcus
GEOMETRIC ANALYSIS TOOLS FOR MESH SEGMENTATION
Surface segmentation, a process which divides a surface into parts, is the basis for many surface manipulation applications which include model metamorphosis, model simplifica- tion, model retrieval, model alignment and texture mapping. This dissertation discusses novel methods for geometric surface analysis and segmentation and applications for these methods. Novel work within this dissertation includes a new 3D mesh segmentation algo- rithm which is referred to as the ridge-walking algorithm. The main benefit of this algo- rithm is that it can dynamically change the criteria it uses to identify surface parts which allows the algorithm to be adjusted to suit different types of surfaces and different segmen- tation goals. The dynamic segmentation behavior allows users to extract three different types of surface regions: (1) regions delineated by convex ridges, (2) regions delineated by concave valleys, and (3) regions delineated by both concave and convex curves. The ridge walking algorithm is quantitatively evaluated by comparing it with competing algo- rithms and human-generated segmentations. The evaluation is accompanied with a detailed geometrical analysis of a select subset of segmentation results to facilitate a better under- standing of the strengths and weaknesses of this algorithm.
The ridge walking algorithm is applied to three domain-specific segmentation prob- lems. The first application uses this algorithm to partition bone fragment surfaces into three semantic parts: (1) the fracture surface, (2) the periosteal surface and (3) the articular surface. Segmentation of bone fragments is an important computational step necessary in developing quantitative methods for bone fracture analysis and for creating computational tools for virtual fracture reconstruction. The second application modifies the 3D ridge walking algorithm so that it can be applied to 2D images. In this case, the 2D image is modeled as a Monge patch and principal curvatures of the intensity surface are computed iv for each image pixel. These principal curvatures are then used by ridge walking algorithm
to segment the image into meaningful parts. The third application uses the ridge walking algorithm to facilitate analysis of virtual 3D terrain models. Specifically, the algorithm is integrated as a part of a larger software system designed to enable users to browse, visualize and analyze 3D geometric data generated by NASA’s Mars Exploratory Rovers Spirit and Opportunity. In this context, the ridge walking algorithm is used to identify surface features such as rocks in the terrain models
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