NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks

Jorstad, Anne; Nigro, Biagio; Calì, Corrado; Wawrzyniak, Marta; Fua, Pascal; Knott, Graham

doi:10.1007/s12021-014-9242-5

Cited by 76 publications

(72 citation statements)

References 13 publications

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“…Blender is an open source 3D computer graphics software used in creative arts and for scientific analysis and visualization [Pyka et al, 2010;Jorstad et al, 2015].…”

Section: Endocranial Volumesmentioning

confidence: 99%

Brain Changes during Phyletic Dwarfing in Elephants and Hippos

Lyras¹

2018

Brain Behav Evol

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Of all known insular mammals, hippos and elephants present the extremes of body size decrease, reducing to 4 and a mere 2% of their ancestral mainland size, respectively. Despite the numerous studies on these taxa, what happens to their relative brain size during phyletic dwarfing is not well known, and results are sometimes conflicting. For example, relative brain size increase has been noted in the Sicilian dwarf elephant, Palaeoloxodon falconeri, whereas relative brain size decrease has been postulated for Malagasy dwarf hippos. Here, I perform an analysis of brain, skull, and body size of 3 insular elephants (Palaeoloxodon “mnaidriensis,” P. tiliensis, and P. falconeri) and 3 insular hippos (Hippopotamus madagascariensis, H. lemerlei, and H. minor) to address this issue and to test whether relative brain size in phyletic dwarf species can be predicted. The results presented here show that the encephalization of all insular elephants and hippos is higher than that of their continental relatives. P. falconeri in particular has an enormous encephalization increase, which has so far not been reported in any other insular mammal. Insular brain size cannot be reliably predicted using either static allometric or ontogenetic scaling models. The results of this study indicate that insular dwarf species follow brain-body allometric relationships different from the expected patterns seen for their mainland relatives.

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“…Blender is an open source 3D computer graphics software used in creative arts and for scientific analysis and visualization [Pyka et al, 2010;Jorstad et al, 2015].…”

Section: Endocranial Volumesmentioning

confidence: 99%

Brain Changes during Phyletic Dwarfing in Elephants and Hippos

Lyras¹

2018

Brain Behav Evol

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“…Amira enables visualization of all analysed data, whereas FIJI and MIB are purely analytical programmes with basic visualization and require a secondary programme to perform computational analysis of the segmentations. Blender (https://www.blender.org/) is one such programme, it is a free graphics software which can be used to reconstruct the objects created in Fiji with the aid of Neuromoph Tools (Jorstad et al ., 2015) (http://cvlab.epfl.ch/NeuroMorph) and perform computational analysis. These were developed specifically to import the objects from Fiji and perform quantification analysis.…”

Section: Methodsmentioning

confidence: 99%

A guide to analysis and reconstruction of serial block face scanning electron microscopy data

Cocks

Taggart

Rind

et al. 2018

Journal of Microscopy

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SummarySerial block face scanning electron microscopy (SBF‐SEM) is a relatively new technique that allows the acquisition of serially sectioned, imaged and digitally aligned ultrastructural data. There is a wealth of information that can be obtained from the resulting image stacks but this presents a new challenge for researchers – how to computationally analyse and make best use of the large datasets produced. One approach is to reconstruct structures and features of interest in 3D. However, the software programmes can appear overwhelming, time‐consuming and not intuitive for those new to image analysis. There are a limited number of published articles that provide sufficient detail on how to do this type of reconstruction. Therefore, the aim of this paper is to provide a detailed step‐by‐step protocol, accompanied by tutorial videos, for several types of analysis programmes that can be used on raw SBF‐SEM data, although there are more options available than can be covered here. To showcase the programmes, datasets of skeletal muscle from foetal and adult guinea pigs are initially used with procedures subsequently applied to guinea pig cardiac tissue and locust brain. The tissue is processed using the heavy metal protocol developed specifically for SBF‐SEM. Trimmed resin blocks are placed into a Zeiss Sigma SEM incorporating the Gatan 3View and the resulting image stacks are analysed in three different programmes, Fiji, Amira and MIB, using a range of tools available for segmentation. The results from the image analysis comparison show that the analysis tools are often more suited to a particular type of structure. For example, larger structures, such as nuclei and cells, can be segmented using interpolation, which speeds up analysis; single contrast structures, such as the nucleolus, can be segmented using the contrast‐based thresholding tools. Knowing the nature of the tissue and its specific structures (complexity, contrast, if there are distinct membranes, size) will help to determine the best method for reconstruction and thus maximize informative output from valuable tissue.

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“…For extracting meshes, we use NeuroMorph [57]. The input data was pre-processed as described in The scientist started the session by getting a high-level overview of the neurites in the dataset using the node-link diagram (Neurite L4, 2D).…”

Section: Datamentioning

confidence: 99%

Abstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cells

Mohammed

Al-Awami

Beyer

et al. 2018

IEEE Trans. Visual. Comput. Graphics

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This thesis presents the design and implementation of Abstractocyte, a system for the visual analysis of astrocytes, and their relation to neurons, in nanoscale volumes of brain tissue. Astrocytes are glial cells, i.e., non-neuronal cells that support neurons and the nervous system. Even though glial cells make up around 50 percent of all cells in the mammalian brain, so far they have been far less studied than neurons. Nevertheless, the study of astrocytes has immense potential for understanding brain function. However, the complex and widely-branching structure of astrocytes requires high-resolution electron microscopy imaging and makes visualization and analysis challenging. Using Abstractocyte, biologists can explore the morphology of astrocytes at various visual abstraction levels, while simultaneously analyzing neighboring neurons and their connectivity. We define a novel, conceptual 2D abstraction space for jointly visualizing astrocytes and neurons. Neuroscientists can choose a joint visualization as a specific point in that 2D abstraction space. Dragging this point allows them to smoothly transition between different abstraction levels in an intuitive manner. We describe the design of Abstractocyte, and present three case studies in which neuroscientists have successfully used our system to assess astrocytic coverage of synapses, glycogen distribution in relation to synapses, and astrocyticmitochondria coverage.

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NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks

Cited by 76 publications

References 13 publications

Brain Changes during Phyletic Dwarfing in Elephants and Hippos

Brain Changes during Phyletic Dwarfing in Elephants and Hippos

A guide to analysis and reconstruction of serial block face scanning electron microscopy data

Abstractocyte: A Visual Tool for Exploring Nanoscale Astroglial Cells

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