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NeuroMorph specifications

Information


Unique identifier OMICS_27982
Name NeuroMorph
Software type Package/Module, Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Medium
Version 2.0
Stability Stable
Requirements
Blender
Maintained Yes

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Documentation


Maintainers


  • person_outline Anne Jorstad <>
  • person_outline Pascal Fua <>
  • person_outline Graham Knott <>
  • person_outline Biagio Nigro <>
  • person_outline Marta Wawrzyniak <>

Additional information


https://wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/NeuroMorph

Publication for NeuroMorph

NeuroMorph in pipelines

 (2)
2015
PMCID: 5042088
PMID: 26179415
DOI: 10.1002/cne.23852

[…] cardona et al., ); ilastik (www.ilastik.org; sommer et al., ) for segmentation and generation of the 3d models; and blender (www.blender.org) for visualization and rendering with the neuromorph package (www.cvlab.ch/neuromorph; jorstad et al., )., we then expanded neuromorph by coding and embedding new add‐ons in blender (see fig. ). the blender/python api enabled us […]

2015
PMCID: 5042088
PMID: 26179415
DOI: 10.1002/cne.23852

[…] analysis in 3d. the choice of tools that allow 3d analysis is very limited; for instance, avizo or imaris can produce measurements and annotations in 3d models. here we have used the package neuromorph (www.cvlab.ch/neuromorph, rrid:scires_000156; jorstad et al., ), which is freely available for measuring meshes in blender (www.blender.org, rrid:nif‐0000‐31943), a 3d modeling software […]


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NeuroMorph in publications

 (8)
PMCID: 5804147
PMID: 29430519
DOI: 10.1523/ENEURO.0298-17.2017

[…] and the surface distribution of individual dat molecules. the reconstructed region contained 13 axon terminals (). the corresponding volumes and surface areas (listed in ) were calculated using the neuromorph (), a blender add-on that uses triangular meshes to evaluate the surface area and corresponding normal to determine the volume of each tetrahedron. the total volume occupied by the 13 axon […]

PMCID: 5947172
PMID: 29333754
DOI: 10.1111/jmi.12676

[…] 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., ) (http://cvlab.epfl.ch/neuromorph) and perform computational analysis. these were developed specifically to import the objects from fiji and perform quantification analysis. opening the segmented 3d objects via these tools […]

PMCID: 5675596
PMID: 29058678
DOI: 10.7554/eLife.29315.018

[…] ; ) and the structures of interest segmented in the trakem2 part of the software (). models were then exported to the blender software (blender foundation, amsterdam; http://www.blender.org), and the neuromorph toolset (http://neuromorph.epfl.ch; ) was used to measure axon cross-section areas, bouton and mitochondrial volumes, and psd surface areas. the beginning and end of each bouton were define […]

PMCID: 5400503
PMID: 28346140
DOI: 10.7554/eLife.24364.020

[…] the neurite or where no descending axon could be found. the remaining 15 cells were imaged at 92 × 92 × 500 nm3 voxel size using a transmitted light brightfield microscope () and reconstructed using neuromorph (see materials and methods) (, ; ). in agreement with other observations (; ; ), we found that hvc(ra) dendrites were compact, with 95.0 ± 2.0% (sem) of the dendritic path found within 100 […]

PMCID: 5322215
PMID: 28271040
DOI: 10.1016/j.nicl.2016.12.018

[…] produced by spm. spm gm loads. we use the publicly available spm12 package to provide tissue concentrations maps.gif gm loads. the geodesic information flow (gif) algorithm () used to produce the neuromorph parcellations (see ) jointly estimates various tissue concentrations maps. we included the resulting gm maps as an alternative to those of spm.anatomical region volumes. the volumes […]


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NeuroMorph institution(s)
Computer Vision Lab, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland; Centre for Electron Microscopy, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland; International Institute of Molecular and Cell Biology, Warsaw, Poland
NeuroMorph funding source(s)
Supported by the Novartis Foundation for Medical-Biological Research and EU ERC MicroNano Project.

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