A morphology repair tool
Project description
NeuroR
Introduction
NeuroR is a collection of tools to repair morphologies.
You can try NeuroR’s functionality on MyBinder:
Cut-plane detection -
Morphology repair -
Acknowledgements
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.
This research was supported by the EBRAINS research infrastructure, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).
Citation
Cite NeuroR with the following DOI:
NeuroR implements the methods discussed in the following paper:
Anwar H., Riachi I., Schürmann F., Markram H. (2009). “An approach to capturing neuron morphological diversity,” in Computational Neuroscience: Realistic Modeling for Experimentalistsed. De Schutter E., editor. (Cambridge: The MIT Press) 211–232
Morphology repair with NeuroR
There are presently three types of repair which are outlined below.
Sanitization
This is the process of sanitizing a morphological file. It currently:
ensures it can be loaded with MorphIO
raises if the morphology has no soma or of invalid format
removes unifurcations
set negative diameters to zero
raises if the morphology has a neurite whose type changes along the way
removes segments with near zero lengths (shorter than 1e-4)
Note: more functionality may be added in the future
Cut plane repair
The cut plane repair aims at regrowing part of a morphologies that have been cut out when the cell has been experimentally sliced.
neuror cut-plane repair contains the collection of CLIs to perform this repair.
Additionally, there are CLIs for the cut plane detection and writing detected cut planes to JSON files:
If the cut plane is aligned with one of the X, Y or Z axes, the cut plane detection can be done automatically with the CLIs:
neuror cut-plane file
neuror cut-plane folderIf the cut plane is not one the X, Y or Z axes, the detection has to be performed through the helper web application that can be launched with the following CLI:
neuror cut-plane hintUnravelling
Unravelling is the action of “stretching” the cell that has been shrunk because of the dehydratation caused by the slicing.
The unravelling CLI sub-group is:
neuror unravelThe unravelling algorithm can be described as follows:
Segments are unravelled iteratively.
Each segment direction is replaced by the averaged direction in a sliding window around this segment.
The original segment length is preserved.
The start position of the new segment is the end of the latest unravelled segment.
Installation
NeuroR is distributed as a Python package available on PyPi:
$ pip install --pre neuror[plotly]Note: NeuroR relies on the experimental version 2 of NeuroM, hence the --pre option.
Only Python 3.6 and above are supported.
Prior to running pip install, we recommend updating pip in your virtual environment unless you have a compelling reason not to do it:
$ pip install --upgrade pip setuptoolsBuilding BlueRepairSDK from sources
To install the old BlueRepairSDK, use this script:
#!/bin/bash
##########
# BBPSDK #
##########
git clone ssh://bbpcode.epfl.ch/common/BBPSDK --recursive
cd BBPSDK
git checkout 7ccfd867b43746909ac3429cf44e2e4014431bbf
git submodule update
cmake -DCLONE_SUBPROJECTS=ON
sed -i 's/add_subdirectory(tests)/#add_subdirectory(tests)/' Lunchbox/CMakeLists.txt
# Remove a word (2nd argument) from all files in a folder (1st argument) and its subfolder
delete_recursive() {
find $1 \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i "s/$2//g"
}
delete_recursive . -Wextra
delete_recursive . -Wall
delete_recursive . -pedantic
make
sudo make install
cd ..
#################
# BlueRepairSDK #
#################
git clone ssh://bbpcode.epfl.ch/platform/BlueRepairSDK
cd BlueRepairSDK
make buildContributing
If you want to improve the project or you see any issue, every contribution is welcome. Please check the contribution guidelines for more information.
License
NeuroR is licensed under the terms of the GNU Lesser General Public License version 3. Refer to COPYING.LESSER and COPYING for details.
Copyright (c) 2019-2021 Blue Brain Project/EPFL
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