Packages made by Yaroslav Halchenko <debian@onerussian.com>

afni

• afni (toolkit for analyzing and visualizing functional MRI data)

• afni-common (miscellaneous scripts and data files for AFNI)

• afni-dbg (debug symbols for AFNI)

• afni-dev (header and static libraries for AFNI plugin development)

afni-data

• afni-atlases (standard space brain atlases for AFNI)

ants

• ants (advanced normalization tools for brain and image analysis)

biosig4c++

• biosig-tools (format conversion tools for biomedical data formats)

• libbiosig-dev (I/O library for biomedical data - development files)

• libbiosig1 (I/O library for biomedical data - dynamic library)

• libbiosig1-dbg (I/O library for biomedical data - debug symbols)

• octave-biosig (Octave bindings for BioSig library)

• python-biosig (Python bindings for BioSig library)

brian

• python-brian (simulator for spiking neural networks)

• python-brian-doc (simulator for spiking neural networks - documentation)

• python-brian-lib (simulator for spiking neural networks – extensions)

btrbk

• btrbk (backup tool for btrfs subvolumes)

caret

• caret (Computerized Anatomical Reconstruction and Editing Toolkit)

caret-data

• caret-data (common data files for Caret)

cctools

• coop-computing-tools (cooperative computing tools)

• coop-computing-tools-dev (libraries and header files for coop-computing-tools)

• coop-computing-tools-doc (documentation for coop-computing-tools)

• python-workqueue (cooperative computing tools work queue Python bindings)

cde

• cde (package everything required to execute a Linux command on another computer)

cmtk

• cmtk (Computational Morphometry Toolkit)

con-duct

• con-duct (lightweight wrapper to collect execution data for a command)

connectome-workbench

• connectome-workbench (brain visualization, analysis and discovery tool)

• connectome-workbench-dbg (brain visualization, analysis and discovery tool – debug symbols)

convert3d

• convert3d (tool(s) for converting 3D images between common file formats)

cython

• cython (C-Extensions for Python)

• cython-dbg (C-Extensions for Python - debug build)

datalad

• datalad (data files management and distribution platform)

• python3-datalad (data files management and distribution platform)

dcm2niix

• dcm2niix (converts DICOM and PAR/REC files into the NIfTI format)

dcmstack

• python3-dcmstack (DICOM to NIfTI conversion - python3 package)

debruijn

• debruijn (De Bruijn cycle generator)

dicomnifti

• dicomnifti (converts DICOM files into the NIfTI format)

dipy

• python-dipy (Python library for the analysis of diffusion MRI datasets)

• python-dipy-doc (Python library for the analysis of diffusion MRI datasets – documentation)

• python-dipy-lib (Python library for the analysis of diffusion MRI datasets – extensions)

diskcache

• python3-diskcache (Python module for Disk and file backed persistent cache)

dmtcp

• dmtcp (Checkpoint/Restart functionality for Linux processes)

• dmtcp-dbg (Debug package for dmtcp)

eeglab11

• eeglab11-sampledata (sample EEG data for EEGLAB tutorials)

• matlab-eeglab11 (electrophysiological data analysis)

freeipmi

• freeipmi (GNU implementation of the IPMI protocol)

• freeipmi-bmc-watchdog (GNU implementation of the IPMI protocol - BMC watchdog)

• freeipmi-common (GNU implementation of the IPMI protocol - common files)

• freeipmi-ipmidetect (GNU IPMI - IPMI node detection tool)

• freeipmi-ipmiseld (GNU IPMI - IPMI node detection tool)

• freeipmi-tools (GNU implementation of the IPMI protocol - tools)

• libfreeipmi-dev (GNU IPMI - development package)

• libfreeipmi16 (GNU IPMI - libraries)

• libipmiconsole-dev (GNU IPMI - ipmiconsole development package)

• libipmiconsole2 (GNU IPMI - Serial-over-Lan library)

• libipmidetect-dev (GNU IPMI - ipmidetect development package)

• libipmidetect0 (GNU IPMI - IPMI node detection library)

• libipmimonitoring-dev (GNU IPMI - ipmimonitoring development package)

• libipmimonitoring5a (GNU IPMI - Sensor monitoring library)

fsl

• fsl (transitional dummy package)

• fsl-5.0 (transitional dummy package)

• fsl-5.0-core (analysis tools for FMRI, MRI and DTI brain imaging)

• fsl-core (metapackage for the latest version of FSL)

fsl-feeds

• fsl-feeds (FSL Evaluation and Example Data Suite)

fsldata

• fsl-5.0-doc-wiki (FSL documentation wiki)

• fsl-atlases (FSL’s MNI152 standard space stereotaxic brain atlases)

• fsl-bangor-cerebellar-atlas (probabilistic atlas of the human cerebellum)

• fsl-first-data (model data for FIRST subcortical brain segmentation)

• fsl-harvard-oxford-atlases (probabilistic atlas of human cortical brain areas (lateralized))

• fsl-harvard-oxford-cortical-lateralized-atlas (probabilistic atlas of human cortical and subcortical brain areas)

• fsl-jhu-dti-whitematter-atlas (human brain white-matter atlas)

• fsl-juelich-histological-atlas (brain atlas based on cyto- and myelo-architectonic segmentations)

• fsl-mni-structural-atlas (hand-segmented single-subject human brain atlas)

• fsl-mni152-templates (MNI152 stereotaxic brain templates for FSL)

• fsl-oxford-striatal-atlas (probabilistic atlas of the human brain’s sub-striatal regions)

• fsl-oxford-thalamic-connectivity-atlas (probabilistic brain atlas of thalamic white-matter connectivity)

• fsl-possum-data (sequence templates for the POSSUM MRI-simulator)

• fsl-resting-connectivity-parcellation-atlases (brain parcellations based on resting state connectivity)

• fsl-subthalamic-nucleus-atlas (probabilistic subthalamic nucleus atlas)

• fsl-talairach-daemon-atlas (structural anatomy labels of the Talairach atlas)

fsleyes-props

• python-fsleyes-props (Python descriptor framework)

fslmeta

• fsl-5.0-complete (metapackage for the entire FSL suite (tools and data))

• fsl-complete (metapackage for the entire FSL suite (tools and data))

fslview

• fslview (viewer for (f)MRI and DTI data)

• fslview-doc (Documentation for FSLView)

gifticlib

• gifti-bin (tools shipped with the GIFTI library)

• libgiftiio-dev (IO library for the GIFTI cortical surface data format)

• libgiftiio0 (IO library for the GIFTI cortical surface data format)

git-annex-remote-rclone

• git-annex-remote-rclone (rclone-based git annex special remote)

haxby2001

• haxby2001-faceobject (face and object processing in ventral temporal cortex (fMRI))

• haxby2001-faceobject-subject1 (face and object processing in ventral temporal cortex (fMRI))

• haxby2001-faceobject-subject2 (face and object processing in ventral temporal cortex (fMRI))

• haxby2001-faceobject-subject3 (face and object processing in ventral temporal cortex (fMRI))

• haxby2001-faceobject-subject4 (face and object processing in ventral temporal cortex (fMRI))

• haxby2001-faceobject-subject5 (face and object processing in ventral temporal cortex (fMRI))

• haxby2001-faceobject-subject6 (face and object processing in ventral temporal cortex (fMRI))

hdmf

• python3-hdmf (Hierarchical Data Modeling Framework)

heudiconv

• heudiconv (DICOM converter with support for structure heuristics)

indexed-gzip

• python-indexed-gzip (fast random access of gzip files in Python)

• python3-indexed-gzip (fast random access of gzip files in Python)

itksnap

• itksnap (semi-automatic segmentation of structures in 3D images)

jist

• jist (Java Image Science Toolkit)

json-tricks

• pypy-json-tricks (Python module with extra features for JSON files)

• python-json-tricks (Python module with extra features for JSON files)

• python3-json-tricks (Python module with extra features for JSON files)

klustakwik

• klustakwik (automatic sorting of the samples (spikes) into clusters)

libfreenect

• freenect (library for accessing Kinect device – metapackage)

• libfreenect-bin (library for accessing Kinect device – utilities and samples)

• libfreenect-demos (library for accessing Kinect device – dummy package)

• libfreenect-dev (library for accessing Kinect device – development files)

• libfreenect-doc (library for accessing Kinect device – documentation)

• libfreenect0.5 (library for accessing Kinect device)

libgdf

• gdf-tools (IO library for the GDF – helper tools)

• libgdf-dev (IO library for the GDF – development library)

• libgdf0 (IO library for the GDF (general dataformat for biosignals))

• matlab-gdf (IO library for the GDF – Matlab interface)

• octave-gdf (IO library for the GDF – Octave interface)

matlab-support

• matlab-support (distro integration for local MATLAB installations)

• matlab-support-dev (helpers for packages building MATLAB toolboxes)

mclaren-rhesus-macaque-atlas

• mclaren-rhesus-macaque-atlas (MRI-based brain atlas of the rhesus macaque monkey)

mdp

• python-mdp (Modular toolkit for Data Processing)

• python3-mdp (Modular toolkit for Data Processing)

mipav

• mipav (quantitative analysis and visualization of medical images)

mni-colin27

• mni-colin27-minc (Talairach stereotaxic space template)

• mni-colin27-nifti (Talairach stereotaxic space template)

mni-icbm152-nlin

• mni-icbm152-nlin-2009a (MNI stereotaxic space human brain template)

• mni-icbm152-nlin-2009b (MNI stereotaxic space human brain template)

• mni-icbm152-nlin-2009c (MNI stereotaxic space human brain template)

mpi4py

• python-mpi4py (bindings of the Message Passing Interface (MPI) standard)

• python-mpi4py-dbg (bindings of the MPI standard – debug symbols)

• python-mpi4py-doc (bindings of the MPI standard – documentation)

• python3-mpi4py (bindings of the Message Passing Interface (MPI) standard)

• python3-mpi4py-dbg (bindings of the MPI standard – debug symbols)

mricron

• mricron (magnetic resonance image conversion, viewing and analysis)

• mricron-data (data files for MRIcron)

• mricron-doc (data files for MRIcron)

mrtrix

• mrtrix (diffusion-weighted MRI white matter tractography)

• mrtrix-doc (documentation for mrtrix)

mrtrix3

• mrtrix3 (diffusion-weighted MRI white matter tractography)

• mrtrix3-doc (documentation for mrtrix3)

neo

• python3-neo (Python IO library for electrophysiological data formats)

neurodebian

• neurodebian (neuroscience-oriented distribution - repository configuration)

• neurodebian-archive-keyring (neuroscience-oriented distribution - GnuPG archive keys)

• neurodebian-desktop (neuroscience-oriented distribution - desktop integration)

• neurodebian-dev (neuroscience-oriented distribution - development tools)

• neurodebian-freeze (nd_freeze tool to freeze APT sources to use snapshots)

• neurodebian-popularity-contest (neuroscience-oriented distribution - popcon integration)

neurosynth

• python-neurosynth (large-scale synthesis of functional neuroimaging data)

neurosynth-data

• fsl-neurosynth-atlas (neurosynth - atlas for use with FSL, all 525 terms)

• fsl-neurosynth-top100-atlas (neurosynth - atlas for use with FSL, top 100 terms)

• neurosynth-dataset (neurosynth - dataset of extracted terms and activations)

nibabel

• python-nibabel-doc (documentation for NiBabel)

• python3-nibabel (Python3 bindings to various neuroimaging data formats)

nifticlib

• libnifti-dev (IO libraries for the NIfTI-1 data format)

• libnifti-doc (NIfTI library API documentation)

• libnifti2 (IO libraries for the NIfTI-1 data format)

• nifti-bin (tools shipped with the NIfTI library)

nilearn

• python-nilearn (fast and easy statistical learning on neuroimaging data (Python 2))

• python3-nilearn (fast and easy statistical learning on neuroimaging data (Python 3))

nipy-suite

• nipy-suite (Neuroimaging in Python)

• nipy-suite-doc (Neuroimaging in Python – documentation)

nipype

• python-nipype-doc (Neuroimaging data analysis pipelines in Python3 – documentation)

• python3-nipype (Neuroimaging data analysis pipelines in Python3)

nitime

• python-nitime-doc (timeseries analysis for neuroscience data (nitime) – documentation)

• python3-nitime (timeseries analysis for neuroscience data (nitime))

numdiff

• numdiff (Compare similar files with numeric fields)

numexpr

• python-numexpr (Fast numerical array expression evaluator for Python and NumPy)

• python3-numexpr (Fast numerical array expression evaluator for Python 3 and NumPy)

odin

• libodin-dev (static libraries and header for ODIN sequences)

• mitools (view, convert and perform basic maths with medical image datasets)

• odin (develop, simulate and run magnetic resonance sequences)

openelectrophy

• openelectrophy (data analysis framework for intra- and extra-cellular recordings)

• python-pyssdh (data analysis framework for intra- and extra-cellular recordings)

openmeeg

• libopenmeeg-dev (openmeeg library – development files)

• libopenmeeg1 (library for solving EEG and MEG forward and inverse problems)

• openmeeg-tools (openmeeg library – command line tools)

• python-openmeeg (openmeeg library – Python bindings)

openpyxl

• python-openpyxl (Python module to read/write OpenXML xlsx/xlsm files)

• python3-openpyxl (Python 3 module to read/write OpenXML xlsx/xlsm files)

openwalnut

• libopenwalnut1 (Framework for multi-modal medical and brain data visualization)

• libopenwalnut1-dev (Development files for the OpenWalnut visualization framework)

• libopenwalnut1-doc (Developer documentation for the OpenWalnut visualization framework)

• openwalnut-modules (Loaders, algorithms and visualization modules for OpenWalnut)

• openwalnut-qt4 (Qt based user interface for OpenWalnut)

pandas

• python-pandas (data structures for “relational” or “labeled” data)

• python-pandas-doc (documentation and examples for pandas)

• python-pandas-lib (low-level implementations and bindings for pandas)

• python3-pandas (data structures for “relational” or “labeled” data - Python 3)

• python3-pandas-lib (low-level implementations and bindings for pandas - Python 3)

patsy

• python-patsy (statistical models in Python using symbolic formulas)

• python-patsy-doc (documentation and examples for patsy)

• python3-patsy (statistical models in Python using symbolic formulas)

pprocess

• python-pprocess (elementary parallel programming for Python)

psychopy

• psychopy (environment for creating psychology stimuli in Python)

psychtoolbox-3

• octave-psychtoolbox-3 (toolbox for vision research – Octave bindings)

• psychtoolbox-3-common (toolbox for vision research – arch/interpreter independent part)

• psychtoolbox-3-dbg (toolbox for vision research – debug symbols for binaries)

• psychtoolbox-3-lib (toolbox for vision research – arch-specific parts)

psychtoolbox-3-nonfree

• matlab-psychtoolbox-3 (toolbox for vision research – Matlab bindings)

• matlab-psychtoolbox-3-nonfree (toolbox for vision research – Matlab binary blobs)

• octave-psychtoolbox-3-nonfree (toolbox for vision research – Octave binary blobs)

pycharm-community-sloppy

• pycharm-community-sloppy (PyCharm IDE (sloppy packaging))

pydicom

• python-dicom (transitional package for python-pydicom)

• python-pydicom (DICOM medical file reading and writing (Python 2))

• python-pydicom-doc (DICOM medical file reading and writing (documentation))

• python3-dicom (transitional package for python3-pydicom)

• python3-pydicom (DICOM medical file reading and writing (Python 3))

pyepl

• python-pyepl (module for coding psychology experiments in Python)

• python-pyepl-common (module for coding psychology experiments in Python)

pyglet

• python3-pyglet (cross-platform windowing and multimedia library (Python 3))

pymc

• python-pymc (Bayesian statistical models and fitting algorithms)

• python-pymc-doc (Bayesian statistical models and fitting algorithms)

pymvpa

• python-mvpa (multivariate pattern analysis with Python)

• python-mvpa-doc (documentation and examples for PyMVPA)

• python-mvpa-lib (low-level implementations and bindings for PyMVPA)

pymvpa2

• python-mvpa2 (multivariate pattern analysis with Python v. 2)

• python-mvpa2-doc (documentation and examples for PyMVPA v. 2)

• python-mvpa2-lib (low-level implementations and bindings for PyMVPA v. 2)

pymvpa2-tutorialdata

• python-mvpa2-tutorialdata (data files for the PyMVPA tutorial)

pynifti

• python-nifti (Python interface to the NIfTI I/O libraries)

pynn

• python-pynn (simulator-independent specification of neuronal network models)

pynwb

• python3-pynwb (Python library for working with Neurodata in the NWB format)

pyoptical

• python-pyoptical (python interface to the CRS ‘OptiCAL’ photometer)

pysurfer

• python-surfer (visualize Freesurfer’s data in Python)

pytables

• python-tables (hierarchical database for Python based on HDF5)

• python-tables-data (hierarchical database for Python based on HDF5 - test data)

• python-tables-dbg (hierarchical database for Python based on HDF5 (debug extension))

• python-tables-doc (hierarchical database for Python based on HDF5 - documentation)

• python-tables-lib (hierarchical database for Python based on HDF5 (extension))

• python3-tables (hierarchical database for Python3 based on HDF5)

• python3-tables-dbg (hierarchical database for Python 3 based on HDF5 (debug extension))

• python3-tables-lib (hierarchical database for Python3 based on HDF5 (extension))

python-etelemetry

• python3-etelemetry (lightweight Python3 client to communicate with the etelemetry server)

python-git

• python-git-doc (Python library to interact with Git repositories - docs)

• python3-git (Python library to interact with Git repositories - Python 3.x)

python-mne

• python-mne (Python modules for MEG and EEG data analysis)

python-quantities

• python3-quantities (Library for computation of physical quantities with units, based on numpy)

python-smmap

• python-smmap (pure Python implementation of a sliding window memory map manager)

• python3-smmap (pure Python implementation of a sliding window memory map manager)

python-tornado

• python-tornado (scalable, non-blocking web server and tools)

pyxid

• python3-pyxid (interface for Cedrus XID and StimTracker devices)

pyxnat

• python-pyxnat (Interface to access neuroimaging data on XNAT servers)

remake

• remake (GNU make fork with improved error reporting and debugging)

reprozip

• python3-reprozip (modules for the ReproZip packer)

• python3-reprozip-dbg (debug extensions for the ReproZip packer)

• reprozip (tool for reproducing scientific experiments (packer))

rnc2rng

• python3-rnc2rng (RELAX NG Compact to regular syntax conversion library)

rorden-mri-tutorial

• rorden-mri-tutorial (Chris Rorden’s MRI analysis tutorial)

• rorden-mri-tutorial-data (data files for Chris Rorden’s MRI analysis tutorial)

scikit-learn

• python-sklearn (Python modules for machine learning and data mining)

• python-sklearn-doc (documentation and examples for scikit-learn)

• python-sklearn-lib (low-level implementations and bindings for scikit-learn)

• python3-sklearn (Python modules for machine learning and data mining - Python 3)

• python3-sklearn-lib (low-level implementations and bindings for scikit-learn - Python 3)

seaborn

• python-seaborn (statistical visualization library)

• python3-seaborn (statistical visualization library)

sigviewer

• sigviewer (GUI viewer for biosignals such as EEG, EMG, and ECG)

singularity-container

• singularity-container (container platform focused on supporting “Mobility of Compute”)

skimage

• python-skimage (Python modules for image processing)

• python-skimage-doc (Documentation and examples for scikit-image)

• python-skimage-lib (Optimized low-level algorithms for scikit-image)

• python3-skimage (Python 3 modules for image processing)

• python3-skimage-lib (Optimized low-level algorithms for Python 3 scikit-image)

spm8

• matlab-spm8 (analysis of brain imaging data sequences for Matlab)

• spm8-common (analysis of brain imaging data sequences)

• spm8-data (data files for SPM8)

• spm8-doc (manual for SPM8)

spykeutils

• python-spykeutils (utilities for analyzing electrophysiological data)

spykeviewer

• spykeviewer (graphical utility for analyzing electrophysiological data)

sri24-atlas

• sri24-atlas (MRI-based brain atlas of normal adult human brain anatomy)

stabilitycalc

• stabilitycalc (evaluate fMRI scanner stability)

statsmodels

• python-statsmodels (Python module for the estimation of statistical models)

• python-statsmodels-doc (documentation and examples for statsmodels)

• python-statsmodels-lib (low-level implementations and bindings for statsmodels)

• python3-statsmodels (Python3 module for the estimation of statistical models)

• python3-statsmodels-lib (Python3 low-level implementations and bindings for statsmodels)

stimfit

• python-stfio (Python module to read common electrophysiology file formats.)

• stimfit (Program for viewing and analyzing electrophysiological data)

• stimfit-dbg (Debug symbols for stimfit)

testkraut

• testkraut (test and evaluate heterogeneous data processing pipelines)

tigervnc

• tigervnc-common (Virtual network computing; Common software needed by clients and servers)

• tigervnc-scraping-server (Virtual network computing server software)

• tigervnc-standalone-server (Virtual network computing server software)

• tigervnc-viewer (Virtual network computing client software for X)

• tigervnc-xorg-extension (Virtual network computing server software)

vmri-nonfree

• virtual-mri-nonfree (Virtual Magnetic Resonance Imager)

voxbo

• voxbo (processing, statistical analysis, and display of brain imaging data)

xppaut

• xppaut (Phase Plane Plus Auto: Solves many kinds of equations)

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