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There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general. We use the same classification of packages that [neuro.debian.net|NeuroDebian] uses to start with:
There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general.




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! Package !! Summary !! Status !! Comment
! Package !! Summary !! Status !! Comment
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| Example || Example || Example || Example
| {{FpPackage| }} || || Packaged ||  
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| Example || Example || Example || Example
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| Example || Example || Example || Example
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== Packages for Electrophysiology ==
== Packages for Image analysis ==
 
{| class="wikitable"
{| class="wikitable"
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! Package !! Summary !! Status !! Comment
! Package !! Summary !! Status !! Comment
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| Example || Example || Example || Example
| {{FpPackage|ctk }} || The CTK core library for Image analysis || Packaged ||
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| {{FpPackage|dcm2niix }} || Conver neuroimaging data from NIFTI format to DICOM || Packaged ||
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| {{FpPackage|isis }} || Framework to access a large variety of image libraries|| Needs import ||
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| {{FpPackage| libminc }} || Library to work with the MINC file format || Packaged ||
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| {{FpPackage|python-nibabel }} || Python package to access a cacophony of neuro-imaging file formats|| Packaged ||  
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| Example || Example || Example || Example
| {{FpPackage|python-pydicom }} || Read, modify, and write DICOM files with Python|| Packaged ||
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| {{FpPackage|rubygem-nifti }} || Pure-ruby library for handling NIfTI data in Ruby|| Packaged ||  
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| Example || Example || Example || Example
|}
|}
== Packages for Magnetic Reasonance Imaging ==
 
== Packages for Data Analysis ==
{| class="wikitable"
{| class="wikitable"
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! Package !! Summary !! Status !! Comment
! Package !! Summary !! Status !! Comment
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| Example || Example || Example || Example
| {{FpPackage|python-mne }} || Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis || Packaged ||  
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| Example || Example || Example || Example
| {{FpPackage|python-pyactivetwo }} ||Python library for reading signal from BioSemi ActiveTwo EEG device || Packaged ||  
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| Example || Example || Example || Example
|}
|}


== Packages for Modeling of neural systems ==
== Packages for Modeling of neural systems ==
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! Package !! Summary !! Status !! Comment
! Package !! Summary !! Status !! Comment
|-
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| Example || Example || Example || Example
| {{FpPackage| }} || || Packaged ||  
|-
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| Example || Example || Example || Example
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| Example || Example || Example || Example
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== Packages for Neuroscience Datasets ==
 
== Misc Libraries/Utilities ==
 
{| class="wikitable"
{| class="wikitable"
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! Package !! Summary !! Status !! Comment
! Package !! Summary !! Status !! Comment
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| Example || Example || Example || Example
| {{FpPackage|python-neo}} || Represent electrophysiology data in Python || Packaged ||
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| {{FpPackage| DiffusionKurtosisFit }} || Reconstruct Diffusion Kurtosis tensor from Diffusion Weighted MRI || Packaged ||
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| {{FpPackage|getdp }} || Finite element solver || Packaged ||
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| {{FpPackage| gifticlib }} || Refernce IO implementation and tools of the GIFTI XML based file format for cortical surface data || Packaged ||
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| {{FpPackage|nipy-data }} || Test data and brain templates for nipy|| Packaged ||
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| {{FpPackage|openigtlink }} || Reference implementation of OpenIGTLink: a set of message formats and protocols used for data exchange over a local area network|| Packaged ||
|-
| {{FpPackage|petpvc }} || Tools for partial volume correction (PVC) in positron emission tomography (PET)|| Packaged ||
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| {{FpPackage|python-amico }} || Relationships backed by Redis|| Packaged ||  
|-
|-
| Example || Example || Example || Example
| {{FpPackage|python-baker }} || Easy, powerful access to Python functions from the command line|| Packaged ||  
|-
|-
| Example || Example || Example || Example
| {{FpPackage|python-citeproc-py }} || Citations and bibliography formatter|| Packaged ||  
|}
|-
 
| {{FpPackage|python-gradunwarp }} || Gradient Unwarping|| Packaged ||  
== Packages for Neuroscience Education ==
{| class="wikitable"
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! Package !! Summary !! Status !! Comment
| {{FpPackage|python-h5io }} || Read and write simple Python objects using HDF5|| Packaged ||
|-
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| Example || Example || Example || Example
| {{FpPackage|python-interfile }} || Python module for read/write/parse interfile|| Packaged ||  
|-
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| Example || Example || Example || Example
| {{FpPackage|python-klusta }} || Spike detection and automatic clustering for spike sorting|| Packaged ||  
|-
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| Example || Example || Example || Example
|}


== Packages for Psychophysics ==
| {{FpPackage|python-lazyarray }} || A lazily-evaluated numerical array class|| Packaged ||
 
|-
{| class="wikitable"
| {{FpPackage|python-moss }} || Assorted utilities for neuroimaging and cognitive science|| Packaged ||
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| {{FpPackage|python-nixio }} || Python bindings for NIX, the Neuroscience Exchange Format|| Packaged ||
|-
| {{FpPackage|python-pydotplus }} || Python interface to Graphviz's Dot language|| Packaged ||  
|-
|-
! Package !! Summary !! Status !! Comment
| {{FpPackage|python-PyLink }} || Universal communication interface using File-Like API|| Packaged ||
|-
|-
| Example || Example || Example || Example
| {{FpPackage|python-pyoptical }} || Pure Python interface to OptiCAL|| Packaged ||  
|-
|-
| Example || Example || Example || Example
| {{FpPackage|python-pyriemann }} || Covariance matrices manipulaton and Biosignal classification|| Packaged ||  
|-
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| Example || Example || Example || Example
| {{FpPackage|python-pyxid }} || Python library for interfacing with Cedrus XID and StimTracker devices|| Packaged ||  
|}
 
== Libraries/utilities ==
 
{| class="wikitable"
|-
|-
! Package !! Summary !! Status !! Comment
| {{FpPackage|python-quantities }} || Support for physical quantities with units, based on numpy|| Packaged ||
|-
|-
| {{FpPackage|python-neo}} || Represent electrophysiology data in Python || Packaged ||  
| {{FpPackage|python-simplewrap }} || Easy to use wrappers generator for C libraries based on ctypes|| Packaged ||  
|-
|-
| {{FpPackage|ctk }} || The CTK core library for Image analysis || ||  
| {{FpPackage| python-tabulate }} || Pretty-print tabular data in Python, a library and a command-line utility|| Packaged ||  
|-
|-
| {{FpPackage| }} || || ||  
| {{FpPackage| python-transforms3d}} || 3 dimensional spatial transformations|| Packaged ||  
|-
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|}
|}

Revision as of 22:56, 21 June 2018

There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general.


Packages for Distributed Computing

Package Summary Status Comment
[1] Packaged

Packages for Image analysis

Package Summary Status Comment
ctk The CTK core library for Image analysis Packaged
dcm2niix Conver neuroimaging data from NIFTI format to DICOM Packaged
isis Framework to access a large variety of image libraries Needs import
libminc libminc Library to work with the MINC file format Packaged
python-nibabel Python package to access a cacophony of neuro-imaging file formats Packaged
python-pydicom Read, modify, and write DICOM files with Python Packaged
rubygem-nifti Pure-ruby library for handling NIfTI data in Ruby Packaged

Packages for Data Analysis

Package Summary Status Comment
python-mne Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis Packaged
python-pyactivetwo Python library for reading signal from BioSemi ActiveTwo EEG device Packaged


Packages for Modeling of neural systems

Package Summary Status Comment
[2] Packaged


Misc Libraries/Utilities

Package Summary Status Comment
python-neo Represent electrophysiology data in Python Packaged
DiffusionKurtosisFit DiffusionKurtosisFit Reconstruct Diffusion Kurtosis tensor from Diffusion Weighted MRI Packaged
getdp Finite element solver Packaged
gifticlib gifticlib Refernce IO implementation and tools of the GIFTI XML based file format for cortical surface data Packaged
nipy-data Test data and brain templates for nipy Packaged
openigtlink Reference implementation of OpenIGTLink: a set of message formats and protocols used for data exchange over a local area network Packaged
petpvc Tools for partial volume correction (PVC) in positron emission tomography (PET) Packaged
python-amico Relationships backed by Redis Packaged
python-baker Easy, powerful access to Python functions from the command line Packaged
python-citeproc-py Citations and bibliography formatter Packaged
python-gradunwarp Gradient Unwarping Packaged
python-h5io Read and write simple Python objects using HDF5 Packaged
python-interfile Python module for read/write/parse interfile Packaged
python-klusta Spike detection and automatic clustering for spike sorting Packaged
python-lazyarray A lazily-evaluated numerical array class Packaged
python-moss Assorted utilities for neuroimaging and cognitive science Packaged
python-nixio Python bindings for NIX, the Neuroscience Exchange Format Packaged
python-pydotplus Python interface to Graphviz's Dot language Packaged
python-PyLink Universal communication interface using File-Like API Packaged
python-pyoptical Pure Python interface to OptiCAL Packaged
python-pyriemann Covariance matrices manipulaton and Biosignal classification Packaged
python-pyxid Python library for interfacing with Cedrus XID and StimTracker devices Packaged
python-quantities Support for physical quantities with units, based on numpy Packaged
python-simplewrap Easy to use wrappers generator for C libraries based on ctypes Packaged
python-tabulate python-tabulate Pretty-print tabular data in Python, a library and a command-line utility Packaged
python-transforms3d python-transforms3d 3 dimensional spatial transformations Packaged
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