diff --git a/.gitexternals b/.gitexternals
index 16fad18..c372733 100644
--- a/.gitexternals
+++ b/.gitexternals
@@ -1,2 +1,3 @@
 # -*- mode: cmake -*-
 # CMake/common https://github.com/Eyescale/CMake.git 11ee9c1
+# Pydoxine https://github.com/BlueBrain/Pydoxine 69eec7a
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 173c70d..08c4ea1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -9,7 +9,7 @@ project(Brion VERSION 1.9.0)
 set(Brion_VERSION_ABI 7)
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake
-  ${CMAKE_SOURCE_DIR}/CMake/common)
+  ${CMAKE_SOURCE_DIR}/CMake/common ${CMAKE_SOURCE_DIR}/Pydoxine/CMake)
 
 include(GitExternal)
 
@@ -36,6 +36,7 @@ common_find_package(OpenMP)
 common_find_package(PythonInterp)
 common_find_package(PythonLibs)
 common_find_package(Servus REQUIRED)
+common_find_package(Sphinx 1.3)
 common_find_package(vmmlib REQUIRED)
 common_find_package_post()
 
@@ -55,3 +56,5 @@ set(DOXYGEN_EXPAND_AS_DEFINED "BRAIN_API BRION_API")
 set(DOXYGEN_EXTRA_INPUT "${PROJECT_SOURCE_DIR}/README.md ${CMAKE_INSTALL_PREFIX}/include/brain")
 set(DOXYGEN_PREDEFINED_MACROS "BRAIN_API:=")
 include(DoxygenRule)
+
+add_subdirectory(doc/python)
diff --git a/README.md b/README.md
index 38bcff1..8b61bcf 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,8 @@ Brion can be retrieved by cloning the
 The [latest API documentation]
 (http://bluebrain.github.io/Brion-1.9/index.html) can be found on
 [bluebrain.github.io](http://bluebrain.github.io).
+Additional documentation exists for the [Python wrapping of Brain]
+(python/index.html).
 
 To keep track of the changes between releases check the [changelog](@ref Changelog).
 
diff --git a/brain/circuit.h b/brain/circuit.h
index ca950be..4430b90 100644
--- a/brain/circuit.h
+++ b/brain/circuit.h
@@ -48,6 +48,7 @@ class Circuit
 
     /**
      * Opens a circuit for read access.
+     *
      * @param source the URI to the CircuitConfig or BlueConfig file.
      */
     BRAIN_API explicit Circuit( const URI& source );
@@ -66,7 +67,7 @@ class Circuit
      */
     BRAIN_API GIDSet getGIDs( const std::string& target ) const;
 
-    /** @return All GIDs held by the circuit */
+    /** @return The set of all GIDs held by the circuit */
     BRAIN_API GIDSet getGIDs() const;
 
     /**
@@ -118,10 +119,14 @@ class Circuit
      */
     BRAIN_API Strings getElectrophysiologyNames() const;
 
-    /** @return The local to world transformations of the given cells. */
+    /** @return \if pybind A Nx4 numpy array with the \else The \endif
+     *          local to world transformations of the given cells.
+     */
     BRAIN_API Matrix4fs getTransforms( const GIDSet& gids ) const;
 
-    /** @return The local to world rotation of the given cells. */
+    /** @return \if pybind A Nx4 numpy array with the \else The \endif
+     *           local to world rotation of the given cells.
+     */
     BRAIN_API Quaternionfs getRotations( const GIDSet& gids ) const;
 
     /** @return The number of neurons in the circuit. */
@@ -131,8 +136,12 @@ class Circuit
      * Access all afferent synapses of the given GIDs.
      *
      * @param gids the gids to load afferent synapses for
+     * \if pybind
+     * @param prefetch which synapse data to preload
+     * \else
      * @param prefetch which synapse data to load on SynapsesStream.read()
      * @return synapse data stream
+     * \endif
      */
     BRAIN_API SynapsesStream getAfferentSynapses(
         const GIDSet& gids,
@@ -142,8 +151,12 @@ class Circuit
      * Access all efferent synapses of the given GIDs.
      *
      * @param gids the gids to load efferent synapses for
+     * \if pybind
+     * @param prefetch which synapse data to preload
+     * \else
      * @param prefetch which synapse data to load on SynapsesStream.read()
      * @return synapse data stream
+     * \endif
      */
     BRAIN_API SynapsesStream getEfferentSynapses(
         const GIDSet& gids,
@@ -154,8 +167,12 @@ class Circuit
      *
      * @param preGIDs the gids to load the efferent synapses for
      * @param postGIDs the gids to load the afferent synapses for
+     * \if pybind
+     * @param prefetch which synapse data to preload
+     * \else
      * @param prefetch which synapse data to load on SynapsesStream.read()
      * @return synapse data stream
+     * \endif
      */
     BRAIN_API SynapsesStream getProjectedSynapses(
         const GIDSet& preGIDs, const GIDSet& postGIDs,
diff --git a/brain/neuron/morphology.h b/brain/neuron/morphology.h
index 137be68..5d1dcb7 100644
--- a/brain/neuron/morphology.h
+++ b/brain/neuron/morphology.h
@@ -55,6 +55,7 @@ class Morphology : public boost::noncopyable
     /**
      * Create a morphology from a URI, load all the data and transform
      * the points.
+     *
      * @param source URI of the morphology data source.
      * @param transform the transformation matrix to apply to the points.
      *        Radii will not be affected by this transformation.
@@ -65,6 +66,7 @@ class Morphology : public boost::noncopyable
     /**
      * Create a morphology from a brion::Morphology, load all the data
      * and transform the points.
+     *
      * @param morphology the brion::Morphology to load from.
      * @param transform the transformation matrix to apply to the points.
      *        Radii will not be affected by this transformation.
@@ -75,6 +77,7 @@ class Morphology : public boost::noncopyable
 
     /**
      * Create a morphology from a URI and load all the data.
+     *
      * @param source URI of the morphology data source.
      * @throw runtime_error if an inconsistency is detected in the input file.
      */
@@ -82,6 +85,7 @@ class Morphology : public boost::noncopyable
 
     /**
      * Create a morphology from a brion::Morphology and load all the data.
+     *
      * @param morphology the brion::Morphology to load from.
      * @throw runtime_error if an inconsistency is detected in the input file.
      */
@@ -120,6 +124,7 @@ class Morphology : public boost::noncopyable
 
     /**
      * Return the Section with the given id.
+     *
      * @throw runtime_error if the id is out of range or the given id refers to
      * a soma section.
      */
@@ -128,8 +133,10 @@ class Morphology : public boost::noncopyable
     /** Return the object with the information about the neuron soma */
     BRAIN_API Soma getSoma() const;
 
-    /** Return the transformation that was passed to the constructor or the
-        identity matrix is no transformation was given. */
+    /** Return \if pybind a 4x4 numpry arry with \endif
+     *  the transformation that was passed to the constructor or the
+     *  identity matrix is no transformation was given.
+     */
     BRAIN_API const Matrix4f& getTransformation() const;
 
 private:
diff --git a/brain/neuron/section.h b/brain/neuron/section.h
index 53e1b53..b49fca0 100644
--- a/brain/neuron/section.h
+++ b/brain/neuron/section.h
@@ -122,8 +122,11 @@ class Section
     BRAIN_API bool hasParent() const;
 
     /**
-     * Return the parent section of this section.
+     * Return the parent section of this section \if pybind or None if doesn't
+     * have any.\else.
+     *
      * @throw runtime_error is the section doesn't have a parent.
+     * \endif
      */
     BRAIN_API Section getParent() const;
 
diff --git a/brain/neuron/soma.h b/brain/neuron/soma.h
index 1c4e67f..1c8f79b 100644
--- a/brain/neuron/soma.h
+++ b/brain/neuron/soma.h
@@ -63,7 +63,9 @@ class Soma
 
     BRAIN_API Soma& operator=( const Soma& soma );
 
-    /** Return the points of the soma profile. */
+    /** Return the x,y,z and radius of the points of the soma
+      * profile \if pybind as a 4xN numpy array\endif.
+      */
     BRAIN_API Vector4fs getProfilePoints() const;
 
     /** Return the mean distance between the profile points and the centroid. */
diff --git a/brain/python/CMakeLists.txt b/brain/python/CMakeLists.txt
index 479d9f5..1a7010a 100644
--- a/brain/python/CMakeLists.txt
+++ b/brain/python/CMakeLists.txt
@@ -13,25 +13,48 @@ if(NOT Boost_PYTHON${USE_BOOST_PYTHON_VERSION}_LIBRARY OR
   return()
 endif()
 
-set(BRAIN_PYTHON_SOURCE_FILES
-  arrayHelpers.cpp
+include(PythonDocstrings)
+
+set(BRAIN_PYTHON_SOURCES
   brain.cpp
   circuit.cpp
+  synapses.cpp
+  neuron/morphology.cpp
+)
+
+set(__docstrings_sources)
+set(__docstrings_headers)
+# Input files to docstrings need absolute paths.
+foreach(__header ${BRAIN_PUBLIC_HEADERS})
+  list(APPEND __docstrings_headers ${PROJECT_SOURCE_DIR}/brain/${__header})
+endforeach()
+foreach(__source ${BRAIN_PYTHON_SOURCES})
+  list(APPEND __docstrings_sources ${CMAKE_CURRENT_SOURCE_DIR}/${__source})
+endforeach()
+
+set(DOCSTRINGS_INCLUDE_PATH ${PROJECT_BINARY_DIR}/include)
+docstrings(__docstrings_sources __docstrings_headers)
+
+list(APPEND BRAIN_PYTHON_SOURCES
+  arrayHelpers.cpp
   spikeReportWriter.cpp
   spikeReportReader.cpp
   spikes.cpp
-  synapses.cpp
   submodules.cpp
   test.cpp
   neuron/module.cpp
-  neuron/morphology.cpp
+  ${PROJECT_BINARY_DIR}/docstrings/cpp/docstrings.cpp
 )
-include_directories(${PYTHON_INCLUDE_DIRS}
+
+include_directories(${PROJECT_BINARY_DIR}/docstrings/cpp
+                    ${PYTHON_INCLUDE_DIRS}
                     ${PYTHON_NUMPY_INCLUDE_DIR})
 
-add_library(brain_python MODULE ${BRAIN_PYTHON_SOURCE_FILES})
+add_library(brain_python MODULE ${BRAIN_PYTHON_SOURCES})
 common_compile_options(brain_python)
-add_dependencies(brain_python Brain)
+if(TARGET ${PROJECT_NAME}-docstrings)
+  add_dependencies(brain_python Brain ${PROJECT_NAME}-docstrings)
+endif()
 
 target_link_libraries(brain_python
   PRIVATE Brain ${PYTHON_LIBRARIES}
diff --git a/brain/python/brain.cpp b/brain/python/brain.cpp
index 22363f6..7a2e4ed 100644
--- a/brain/python/brain.cpp
+++ b/brain/python/brain.cpp
@@ -25,6 +25,8 @@
 
 #include "arrayHelpers.h"
 
+#include "docstrings.h"
+
 #include <vmmlib/vector.hpp>
 
 namespace brain
@@ -65,12 +67,19 @@ struct URItoString
 
 BOOST_PYTHON_MODULE(_brain)
 {
+#if defined BRION_USE_SPHINX && defined BRION_USE_DOGYXGEN
+    /* Only change the default Boost.Python options for documentation if we
+       are going to get docstrings from doxygen. */
+    boost::python::docstring_options doc_options(true, true, false);
+#endif
+
     boost::python::to_python_converter< servus::URI, URItoString >();
     boost::python::to_python_converter< brain::Vector3f, Vector3fToTuple >();
 
     brain::importArray();
 
-    boost::python::enum_< brain::SynapsePrefetch >( "SynapsePrefetch" )
+    boost::python::enum_< brain::SynapsePrefetch >(
+        "SynapsePrefetch", DOXY_ENUM( brain::SynapsePrefetch ))
         .value( "none", brain::SynapsePrefetch::none )
         .value( "attributes", brain::SynapsePrefetch::attributes )
         .value( "positions", brain::SynapsePrefetch::positions )
diff --git a/brain/python/circuit.cpp b/brain/python/circuit.cpp
index a57c60c..828e603 100644
--- a/brain/python/circuit.cpp
+++ b/brain/python/circuit.cpp
@@ -23,6 +23,7 @@
 #include "arrayHelpers.h"
 #include "helpers.h"
 #include "types.h"
+#include "docstrings.h"
 
 #include <brain/circuit.h>
 #include <brain/synapses.h>
@@ -143,7 +144,7 @@ void export_Circuit()
 {
 
 bp::class_< Circuit, boost::noncopyable, CircuitPtr >
-    circuitWrapper( "Circuit", bp::no_init );
+    circuitWrapper( "Circuit", DOXY_CLASS( brain::Circuit ), bp::no_init );
 
 bp::scope circuitScope = circuitWrapper;
 
@@ -152,29 +153,62 @@ bp::enum_< Circuit::Coordinates >( "Coordinates" )
     .value( "local", Circuit::Coordinates::local )
     ;
 
+const auto selfarg = bp::arg( "self" );
+
+// Do not modify whitespace on DOXY_FN lines
+
 circuitWrapper
-    .def( "__init__", bp::make_constructor( Circuit_initFromURI ))
-    .def( "gids", Circuit_getAllGIDs )
-    .def( "gids", Circuit_getGIDs )
-    .def( "random_gids", Circuit_getRandomTargetGIDs )
-    .def( "random_gids", Circuit_getRandomGIDs )
-    .def( "morphology_uris", Circuit_getMorphologyURIs )
-    .def( "load_morphologies", Circuit_loadMorphologies )
-    .def( "positions", Circuit_getPositions )
-    .def( "morphology_types", Circuit_getMorphologyTypes )
-    .def( "morphology_names", Circuit_getMorphologyNames )
-    .def( "electrophysiology_types", Circuit_getElectrophysiologyTypes )
-    .def( "electrophysiology_names", Circuit_getElectrophysiologyNames )
-    .def( "transforms", Circuit_getTransforms )
-    .def( "rotations", Circuit_getRotations )
-    .def( "num_neurons", &Circuit::getNumNeurons )
+    .def( "__init__", bp::make_constructor( Circuit_initFromURI ),
+          DOXY_FN( brain::Circuit::Circuit(const URI&)))
+    .def( "gids", Circuit_getAllGIDs, ( selfarg ),
+          DOXY_FN( brain::Circuit::getGIDs() const))
+    .def( "gids", Circuit_getGIDs, ( selfarg, bp::arg( "target" )),
+          DOXY_FN( brain::Circuit::getGIDs(const std::string&) const))
+    .def( "random_gids", Circuit_getRandomTargetGIDs,
+          ( selfarg, bp::arg( "fraction" ), bp::arg( "target" )),
+          DOXY_FN( brain::Circuit::getRandomGIDs(float, const std::string&) const))
+    .def( "random_gids", Circuit_getRandomGIDs,
+          ( selfarg, bp::arg( "fraction" )),
+          DOXY_FN( brain::Circuit::getRandomGIDs(float) const))
+    .def( "morphology_uris", Circuit_getMorphologyURIs,
+          ( selfarg, bp::arg( "gids" )),
+          DOXY_FN( brain::Circuit::getMorphologyURIs ))
+    .def( "load_morphologies", Circuit_loadMorphologies,
+          ( selfarg, bp::arg( "gids" ), bp::arg( "coords" )),
+          DOXY_FN( brain::Circuit::loadMorphologies ))
+    .def( "positions", Circuit_getPositions, ( selfarg, bp::arg( "gids" )),
+          DOXY_FN( brain::Circuit::getPositions ))
+    .def( "morphology_types", Circuit_getMorphologyTypes,
+          ( selfarg, bp::arg( "gids" )),
+          DOXY_FN( brain::Circuit::getMorphologyTypes ))
+    .def( "morphology_names", Circuit_getMorphologyNames, ( selfarg ),
+          DOXY_FN( brain::Circuit::getMorphologyNames ))
+    .def( "electrophysiology_types", Circuit_getElectrophysiologyTypes,
+          ( selfarg, bp::arg( "gids" )),
+          DOXY_FN( brain::Circuit::getElectrophysiologyTypes ))
+    .def( "electrophysiology_names", Circuit_getElectrophysiologyNames,
+          ( selfarg),
+          DOXY_FN( brain::Circuit::getElectrophysiologyNames ))
+    .def( "transforms", Circuit_getTransforms,
+          ( selfarg, bp::arg( "gids" )),
+          DOXY_FN( brain::Circuit::getTransforms ))
+    .def( "rotations", Circuit_getRotations,
+          ( selfarg, bp::arg( "gids" )),
+          DOXY_FN( brain::Circuit::getRotations ))
+    .def( "num_neurons", &Circuit::getNumNeurons, ( selfarg ),
+          DOXY_FN( brain::Circuit::getNumNeurons ))
     .def( "afferent_synapses", Circuit_getAfferentSynapses,
-          ( bp::arg( "gids"), bp::arg( "prefetch" ) = SynapsePrefetch::none ))
+          ( selfarg, bp::arg( "gids"),
+            bp::arg( "prefetch" ) = SynapsePrefetch::none ),
+          DOXY_FN( brain::Circuit::getAfferentSynapses ))
     .def( "efferent_synapses", Circuit_getEfferentSynapses,
-          ( bp::arg( "gids"), bp::arg( "prefetch" ) = SynapsePrefetch::none ))
+          ( selfarg, bp::arg( "gids"),
+            bp::arg( "prefetch" ) = SynapsePrefetch::none ),
+          DOXY_FN( brain::Circuit::getEfferentSynapses ))
     .def( "projected_synapses", Circuit_getProjectedSynapses,
-          ( bp::arg( "preGids"), bp::arg( "postGIDs" ),
-            bp::arg( "prefetch" ) = SynapsePrefetch::none ))
+          ( selfarg, bp::arg( "preGids"), bp::arg( "postGIDs" ),
+            bp::arg( "prefetch" ) = SynapsePrefetch::none ),
+          DOXY_FN( brain::Circuit::getProjectedSynapses ))
     ;
 }
 
diff --git a/brain/python/neuron/morphology.cpp b/brain/python/neuron/morphology.cpp
index 6cf0eca..6fb619a 100644
--- a/brain/python/neuron/morphology.cpp
+++ b/brain/python/neuron/morphology.cpp
@@ -22,6 +22,7 @@
 
 #include "../arrayHelpers.h"
 #include "../helpers.h"
+#include "docstrings.h"
 
 #include <brain/neuron/morphology.h>
 #include <brain/neuron/section.h>
@@ -180,40 +181,73 @@ bp::object Morphology_getTransformation( const MorphologyPtr& morphology )
 void export_Morphology()
 {
 
+const auto selfarg = bp::arg( "self" );
+
+// Do not modify whitespace on DOXY_FN lines
+
 bp::class_< SomaWrapper >(
-    "Soma", bp::no_init )
-    .def( "profile_points", Soma_getProfilePoints )
-    .def( "mean_radius", &Soma::getMeanRadius )
-    .def( "centroid", &Soma::getCentroid )
+    "Soma", DOXY_CLASS( brain::neuron::Soma ), bp::no_init )
+    .def( "profile_points", Soma_getProfilePoints, ( selfarg ),
+          DOXY_FN( brain::neuron::Soma::getProfilePoints ))
+    .def( "mean_radius", &Soma::getMeanRadius, ( selfarg ),
+          DOXY_FN( brain::neuron::Soma::getMeanRadius ))
+    .def( "centroid", &Soma::getCentroid, ( selfarg ),
+          DOXY_FN( brain::neuron::Soma::getCentroid ))
     ;
 
 bp::class_< SectionWrapper >(
-    "Section", bp::no_init )
+    "Section", DOXY_CLASS( brain::neuron::Section ), bp::no_init )
     .def( bp::self == bp::self )
-    .def( "id", &Section::getID )
-    .def( "type", &Section::getType )
-    .def( "length", &Section::getLength )
-    .def( "samples", Section_getSamples )
-    .def( "samples", Section_getSamplesFromPositions )
-    .def( "distance_to_soma", &Section::getDistanceToSoma )
-    .def( "sample_distances_to_soma", Section_getSampleDistancesToSoma )
-    .def( "parent", Section_getParent )
-    .def( "children", Section_getChildren )
+    .def( "id", &Section::getID, ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getID ))
+    .def( "type", &Section::getType, ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getType ))
+    .def( "length", &Section::getLength, ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getLength ))
+    .def( "samples", Section_getSamples, ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getSamples() const))
+    .def( "samples", Section_getSamplesFromPositions,
+          ( selfarg, bp::arg( "positions" )),
+          DOXY_FN( brain::neuron::Section::getSamples(const floats&) const))
+    .def( "distance_to_soma", &Section::getDistanceToSoma, ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getDistanceToSoma ))
+    .def( "sample_distances_to_soma", Section_getSampleDistancesToSoma,
+          ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getSampleDistancesToSoma ))
+    .def( "parent", Section_getParent, ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getParent ))
+    .def( "children", Section_getChildren, ( selfarg ),
+          DOXY_FN( brain::neuron::Section::getChildren ))
     ;
 
 bp::class_< Morphology, boost::noncopyable, MorphologyPtr >(
-    "Morphology", bp::no_init )
-    .def( "__init__", bp::make_constructor( Morphology_initFromURI ))
-    .def( "__init__", bp::make_constructor( Morphology_initFromURIAndTransform ))
-    .def( "points", Morphology_getPoints )
-    .def( "sections", Morphology_getSections )
-    .def( "section_types", Morphology_getSectionTypes)
-    .def( "apicals", Morphology_getApicals )
-    .def( "section_ids", Morphology_getSectionIDs )
-    .def( "sections", Morphology_getSectionsByType )
-    .def( "section", Morphology_getSection )
-    .def( "soma", Morphology_getSoma )
-    .def( "transformation", Morphology_getTransformation )
+    "Morphology", DOXY_CLASS( brain::neuron::Morphology ), bp::no_init )
+    .def( "__init__", bp::make_constructor( Morphology_initFromURI ),
+          DOXY_FN( brain::neuron::Morphology::Morphology(const URI&)))
+    .def( "__init__", bp::make_constructor( Morphology_initFromURIAndTransform ),
+          DOXY_FN( brain::neuron::Morphology::Morphology(const URI&, const Matrix4f&)))
+    // The following docstrings are given explictly because the return types
+    // are special and the original documentation uses @sa, which points nowhere.
+    .def( "points", Morphology_getPoints, ( selfarg ),
+          "Return a 4xN numpy array with the x,y,z and radius of all the points of this morphology.")
+    .def( "sections", Morphology_getSections, ( selfarg ),
+          "Return a 2xN numpy array with the parent ID and first point offset of each section." )
+    .def( "section_types", Morphology_getSectionTypes, ( selfarg ),
+          "Return a numpy array with the section types." )
+    .def( "apicals", Morphology_getApicals, ( selfarg ),
+          "Return a 2xN numpy array with the section id and point index of apical points." )
+    .def( "section_ids", Morphology_getSectionIDs,
+          ( selfarg, bp::arg( "types" )),
+          DOXY_FN( brain::neuron::Morphology::getSectionIDs ))
+    .def( "sections", Morphology_getSectionsByType,
+          ( selfarg, bp::arg( "type" )),
+          DOXY_FN( brain::neuron::Morphology::getSections(const SectionTypes&) const))
+    .def( "section", Morphology_getSection, ( selfarg, bp::arg( "id" )),
+          DOXY_FN( brain::neuron::Morphology::getSections(SectionType) const))
+    .def( "soma", Morphology_getSoma, ( selfarg ),
+          DOXY_FN( brain::neuron::Morphology::getSoma ))
+    .def( "transformation", Morphology_getTransformation, ( selfarg ),
+          DOXY_FN( brain::neuron::Morphology::getTransformation ))
     ;
 
 }
diff --git a/brain/python/synapses.cpp b/brain/python/synapses.cpp
index eb90eff..6bdbb33 100644
--- a/brain/python/synapses.cpp
+++ b/brain/python/synapses.cpp
@@ -21,9 +21,10 @@
 
 #include "types.h"
 #include "arrayHelpers.h"
+#include "docstrings.h"
 
 #include <brain/synapses.h>
-#include <brain/synapses.h>
+
 
 #include <vmmlib/vector.hpp>
 
@@ -90,63 +91,115 @@ GET_SYNAPSES_ARRAY_PROPERTY( int, efficacies )
 void export_Synapses()
 {
 
-bp::class_< SynapseWrapper >( "Synapse", bp::no_init )
-    .def( "pre_gid", &Synapse::getPresynapticGID )
-    .def( "pre_section", &Synapse::getPresynapticSectionID )
-    .def( "pre_segment", &Synapse::getPresynapticSegmentID )
-    .def( "pre_distance", &Synapse::getPresynapticDistance )
-    .def( "pre_center_position", &Synapse::getPresynapticCenterPosition )
-    .def( "pre_surface_position", &Synapse::getPresynapticSurfacePosition )
-    .def( "post_gid", &Synapse::getPostsynapticGID )
-    .def( "post_section", &Synapse::getPostsynapticSectionID )
-    .def( "post_segment", &Synapse::getPostsynapticSegmentID )
-    .def( "post_distance", &Synapse::getPostsynapticDistance )
-    .def( "post_center_position", &Synapse::getPostsynapticCenterPosition )
-    .def( "post_surface_position", &Synapse::getPostsynapticSurfacePosition )
-    .def( "delay", &Synapse::getDelay )
-    .def( "conductance", &Synapse::getConductance )
-    .def( "utilization", &Synapse::getUtilization )
-    .def( "depression", &Synapse::getDepression )
-    .def( "facilitation", &Synapse::getFacilitation )
-    .def( "decay", &Synapse::getDecay )
-    .def( "efficacy", &Synapse::getEfficacy )
+const auto selfarg = bp::arg( "self" );
+
+bp::class_< SynapseWrapper >( "Synapse",
+                              DOXY_CLASS( brain::Synapse ), bp::no_init )
+    .def( "pre_gid", &Synapse::getPresynapticGID, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPresynapticGID ))
+    .def( "pre_section", &Synapse::getPresynapticSectionID, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPresynapticSectionID ))
+    .def( "pre_segment", &Synapse::getPresynapticSegmentID, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPresynapticSegmentID ))
+    .def( "pre_distance", &Synapse::getPresynapticDistance, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPresynapticDistance ))
+    .def( "pre_center_position", &Synapse::getPresynapticCenterPosition,
+          ( selfarg ), DOXY_FN( brain::Synapse::getPresynapticCenterPosition ))
+    .def( "pre_surface_position", &Synapse::getPresynapticSurfacePosition,
+          ( selfarg ), DOXY_FN( brain::Synapse::getPresynapticSurfacePosition ))
+    .def( "post_gid", &Synapse::getPostsynapticGID, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPostsynapticGID ))
+    .def( "post_section", &Synapse::getPostsynapticSectionID, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPostsynapticSectionID ))
+    .def( "post_segment", &Synapse::getPostsynapticSegmentID, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPostsynapticSegmentID ))
+    .def( "post_distance", &Synapse::getPostsynapticDistance, ( selfarg ),
+          DOXY_FN( brain::Synapse::getPostsynapticDistance ))
+    .def( "post_center_position", &Synapse::getPostsynapticCenterPosition,
+          ( selfarg ), DOXY_FN( brain::Synapse::getPostsynapticCenterPosition ))
+    .def( "post_surface_position", &Synapse::getPostsynapticSurfacePosition,
+          ( selfarg ), DOXY_FN( brain::Synapse::getPostsynapticSurfacePosition ))
+    .def( "delay", &Synapse::getDelay, ( selfarg ),
+          DOXY_FN( brain::Synapse::getDelay ))
+    .def( "conductance", &Synapse::getConductance, ( selfarg ),
+          DOXY_FN( brain::Synapse::getConductance ))
+    .def( "utilization", &Synapse::getUtilization, ( selfarg ),
+          DOXY_FN( brain::Synapse::getUtilization ))
+    .def( "depression", &Synapse::getDepression, ( selfarg ),
+          DOXY_FN( brain::Synapse::getDepression ))
+    .def( "facilitation", &Synapse::getFacilitation, ( selfarg ),
+          DOXY_FN( brain::Synapse::getFacilitation ))
+    .def( "decay", &Synapse::getDecay, ( selfarg ),
+          DOXY_FN( brain::Synapse::getDecay ))
+    .def( "efficacy", &Synapse::getEfficacy, ( selfarg ),
+          DOXY_FN( brain::Synapse::getEfficacy ))
     ;
 
-bp::class_< SynapsesWrapper >( "Synapses", bp::no_init )
+bp::class_< SynapsesWrapper >( "Synapses", DOXY_CLASS( brain::Synapses ),
+                               bp::no_init )
     .def( "__nonzero__", nonzero )
     .def( "__len__", &Synapses::size )
     .def( "__getitem__", Synapses_get )
     // There is no need to wrap the iterator, Python provides one out of the
     // box thanks to __len__ and __getitem__
-    .def( "empty", &Synapses::empty )
-    .def( "indices", Synapses_indices )
-    .def( "pre_gids", Synapses_preGIDs )
-    .def( "pre_section_ids", Synapses_preSectionIDs )
-    .def( "pre_segment_ids", Synapses_preSegmentIDs )
-    .def( "pre_distances", Synapses_preDistances )
-    .def( "pre_surface_x_positions", Synapses_preSurfaceXPositions )
-    .def( "pre_surface_y_positions", Synapses_preSurfaceYPositions )
-    .def( "pre_surface_z_positions", Synapses_preSurfaceZPositions )
-    .def( "pre_center_x_positions", Synapses_preCenterXPositions )
-    .def( "pre_center_y_positions", Synapses_preCenterYPositions )
-    .def( "pre_center_z_positions", Synapses_preCenterZPositions )
-    .def( "post_gids", Synapses_postGIDs )
-    .def( "post_section_ids", Synapses_postSectionIDs )
-    .def( "post_segment_ids", Synapses_postSegmentIDs )
-    .def( "post_distances", Synapses_postDistances )
-    .def( "post_surface_x_positions", Synapses_postSurfaceXPositions )
-    .def( "post_surface_y_positions", Synapses_postSurfaceYPositions )
-    .def( "post_surface_z_positions", Synapses_postSurfaceZPositions )
-    .def( "post_center_x_positions", Synapses_postCenterXPositions )
-    .def( "post_center_y_positions", Synapses_postCenterYPositions )
-    .def( "post_center_z_positions", Synapses_postCenterZPositions )
-    .def( "delays", Synapses_delays )
-    .def( "conductances", Synapses_conductances )
-    .def( "utilizations", Synapses_utilizations )
-    .def( "depressions", Synapses_depressions )
-    .def( "facilitations", Synapses_facilitations )
-    .def( "decays", Synapses_decays )
-    .def( "efficacies", Synapses_efficacies )
+    .def( "empty", &Synapses::empty, ( selfarg ),
+          DOXY_FN( brain::Synapses::empty ))
+    .def( "indices", Synapses_indices, ( selfarg ),
+          DOXY_FN( brain::Synapses::indices ))
+    .def( "pre_gids", Synapses_preGIDs, ( selfarg ),
+          DOXY_FN( brain::Synapses::preGIDs ))
+    .def( "pre_section_ids", Synapses_preSectionIDs, ( selfarg ),
+          DOXY_FN( brain::Synapses::preSectionIDs ))
+    .def( "pre_segment_ids", Synapses_preSegmentIDs, ( selfarg ),
+          DOXY_FN( brain::Synapses::preSegmentIDs ))
+    .def( "pre_distances", Synapses_preDistances, ( selfarg ),
+          DOXY_FN( brain::Synapses::preDistances ))
+    .def( "pre_surface_x_positions", Synapses_preSurfaceXPositions,
+          ( selfarg ), DOXY_FN( brain::Synapses::preSurfaceXPositions ))
+    .def( "pre_surface_y_positions", Synapses_preSurfaceYPositions,
+          ( selfarg ), DOXY_FN( brain::Synapses::preSurfaceYPositions ))
+    .def( "pre_surface_z_positions", Synapses_preSurfaceZPositions,
+          ( selfarg ), DOXY_FN( brain::Synapses::preSurfaceZPositions ))
+    .def( "pre_center_x_positions", Synapses_preCenterXPositions, ( selfarg ),
+          DOXY_FN( brain::Synapses::preCenterXPositions ))
+    .def( "pre_center_y_positions", Synapses_preCenterYPositions, ( selfarg ),
+          DOXY_FN( brain::Synapses::preCenterYPositions ))
+    .def( "pre_center_z_positions", Synapses_preCenterZPositions, ( selfarg ),
+          DOXY_FN( brain::Synapses::preCenterZPositions ))
+    .def( "post_gids", Synapses_postGIDs, ( selfarg ),
+          DOXY_FN( brain::Synapses::postGIDs ))
+    .def( "post_section_ids", Synapses_postSectionIDs, ( selfarg ),
+          DOXY_FN( brain::Synapses::postSectionIDs ))
+    .def( "post_segment_ids", Synapses_postSegmentIDs, ( selfarg ),
+          DOXY_FN( brain::Synapses::postSegmentIDs ))
+    .def( "post_distances", Synapses_postDistances, ( selfarg ),
+          DOXY_FN( brain::Synapses::postDistances ))
+    .def( "post_surface_x_positions", Synapses_postSurfaceXPositions,
+          ( selfarg ), DOXY_FN( brain::Synapses::postSurfaceXPositions ))
+    .def( "post_surface_y_positions", Synapses_postSurfaceYPositions,
+          ( selfarg ), DOXY_FN( brain::Synapses::postSurfaceYPositions ))
+    .def( "post_surface_z_positions", Synapses_postSurfaceZPositions,
+          ( selfarg ), DOXY_FN( brain::Synapses::postSurfaceZPositions ))
+    .def( "post_center_x_positions", Synapses_postCenterXPositions, ( selfarg ),
+          DOXY_FN( brain::Synapses::postCenterXPositions ))
+    .def( "post_center_y_positions", Synapses_postCenterYPositions, ( selfarg ),
+          DOXY_FN( brain::Synapses::postCenterYPositions ))
+    .def( "post_center_z_positions", Synapses_postCenterZPositions, ( selfarg ),
+          DOXY_FN( brain::Synapses::postCenterZPositions ))
+    .def( "delays", Synapses_delays, ( selfarg ),
+          DOXY_FN( brain::Synapses::delays ))
+    .def( "conductances", Synapses_conductances, ( selfarg ),
+          DOXY_FN( brain::Synapses::conductances ))
+    .def( "utilizations", Synapses_utilizations, ( selfarg ),
+          DOXY_FN( brain::Synapses::utilizations ))
+    .def( "depressions", Synapses_depressions, ( selfarg ),
+          DOXY_FN( brain::Synapses::depressions ))
+    .def( "facilitations", Synapses_facilitations, ( selfarg ),
+          DOXY_FN( brain::Synapses::facilitations ))
+    .def( "decays", Synapses_decays, ( selfarg ),
+          DOXY_FN( brain::Synapses::decays ))
+    .def( "efficacies", Synapses_efficacies, ( selfarg ),
+          DOXY_FN( brain::Synapses::efficacies ))
     ;
 
 }
diff --git a/brain/synapses.h b/brain/synapses.h
index 4b6b4bb..9174a56 100644
--- a/brain/synapses.h
+++ b/brain/synapses.h
@@ -34,6 +34,9 @@ namespace brain
  * per-array access on the various synapses attributes. Data which was not
  * prefetched will be loaded on-demand.
  *
+ * This container can be iterated as well as random accessed using the
+ * operator [].
+ *
  * This class is thread-safe, moveable and copyable.
  */
 class Synapses
diff --git a/doc/Changelog.md b/doc/Changelog.md
index fc87dcd..4980e4a 100644
--- a/doc/Changelog.md
+++ b/doc/Changelog.md
@@ -3,6 +3,8 @@ Changelog {#Changelog}
 
 # Release 1.9.0 (git master)
 
+* [107](https://github.com/BlueBrain/Brion/pull/107):
+  Added Sphinx generated documentation of the brain python module.
 * [102](https://github.com/BlueBrain/Brion/pull/102):
   Use PersistentMap for caching synapse positions loaded from brain::Circuit
 * [94](https://github.com/BlueBrain/Brion/pull/94):
diff --git a/doc/feature/compartmentReport.md b/doc/feature/compartmentReport.md
index 169deda..864157e 100644
--- a/doc/feature/compartmentReport.md
+++ b/doc/feature/compartmentReport.md
@@ -1,4 +1,4 @@
-Additions to compartmentReport to support ZeroEQ streams
+Additions to compartmentReport to support ZeroEQ streams {#compartmentReport}
 ============
 
 ## Motivation
diff --git a/doc/feature/compartmentReportMPI.md b/doc/feature/compartmentReportMPI.md
index 3fc9f61..75c503c 100644
--- a/doc/feature/compartmentReportMPI.md
+++ b/doc/feature/compartmentReportMPI.md
@@ -1,4 +1,4 @@
-Compartment report writing from MPI applications
+Compartment report writing from MPI applications {#compartmentReportMPI}
 ============
 
 This feature is a modification of the CompartmentReport to allow MPI
diff --git a/doc/feature/feature.md b/doc/feature/feature.md
new file mode 100644
index 0000000..82c9022
--- /dev/null
+++ b/doc/feature/feature.md
@@ -0,0 +1,8 @@
+Feature specifications {#FeatureSpecs}
+======================
+
+* @subpage compartmentReport
+* @subpage compartmentReportMPI
+* @subpage morphology11
+* @subpage spikeReport
+* @subpage brainSynapses
diff --git a/doc/feature/morphology11.md b/doc/feature/morphology11.md
index 1be488e..fbcde61 100644
--- a/doc/feature/morphology11.md
+++ b/doc/feature/morphology11.md
@@ -1,4 +1,4 @@
-Implementing Morphology version 1.1, support for glia cells
+Implementing Morphology version 1.1, support for glia cells {#morphology11}
 ============
 
 The current morphology version 1 specification and implementation is tailored
diff --git a/doc/feature/spikeReport.md b/doc/feature/spikeReport.md
index 4d0053a..347429d 100644
--- a/doc/feature/spikeReport.md
+++ b/doc/feature/spikeReport.md
@@ -1,4 +1,4 @@
-Redesign of the SpikeReport and Spikes container
+Redesign of the SpikeReport and Spikes container {#spikeReport}
 ============
 
 The current design of the SpikeReport has several flaws that need to be
diff --git a/doc/feature/synapses.md b/doc/feature/synapses.md
index 8bd8bfe..0e85de7 100644
--- a/doc/feature/synapses.md
+++ b/doc/feature/synapses.md
@@ -1,4 +1,4 @@
-Synapse support in Brain
+Synapse support in Brain {#brainSynapses}
 ============
 
 The low-level data access for synapses provided by Brion needs a complementary
diff --git a/doc/python/CMakeLists.txt b/doc/python/CMakeLists.txt
new file mode 100644
index 0000000..803aae5
--- /dev/null
+++ b/doc/python/CMakeLists.txt
@@ -0,0 +1,24 @@
+# Copyright (c) 2016, EPFL/Blue Brain Project
+#                     Juan Hernando Vieites <juan.hernando@epfl.ch>
+#
+# This file is part of Brion <https://github.com/BlueBrain/Brion>
+#
+
+if(NOT SPHINX_FOUND)
+  return()
+endif()
+
+configure_file(conf.py.in ${PROJECT_BINARY_DIR}/doc/python/conf.py)
+
+file(COPY index.rst DESTINATION ${PROJECT_BINARY_DIR}/doc/python)
+
+add_custom_target(${PROJECT_NAME}-python-doc-html
+  ${SPHINX_EXECUTABLE} -b html . ${PROJECT_BINARY_DIR}/doc/html/python
+  WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/doc/python
+  DEPENDS index.rst conf.py.in
+  COMMENT "Generating Python documentation using Sphinx" VERBATIM)
+set_target_properties(${PROJECT_NAME}-python-doc-html PROPERTIES
+  EXCLUDE_FROM_DEFAULT_BUILD ON FOLDER "doxygen")
+
+add_dependencies(${PROJECT_NAME}-python-doc-html brain_python)
+add_dependencies(${PROJECT_NAME}-doxygen ${PROJECT_NAME}-python-doc-html)
diff --git a/doc/python/conf.py.in b/doc/python/conf.py.in
new file mode 100644
index 0000000..ef035c1
--- /dev/null
+++ b/doc/python/conf.py.in
@@ -0,0 +1,189 @@
+# Copyright (c) 2016, EPFL/Blue Brain Project
+#                     Juan Hernando Vieites <juan.hernando@epfl.ch>
+#
+# This file is part of Brion <https://github.com/BlueBrain/Brion>
+#
+
+import sys, os
+import re
+
+sys.path.append('${CMAKE_BINARY_DIR}/lib')
+sys.path.append('${PROJECT_BINARY_DIR}/doc/python')
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc']
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Brain'
+copyright = u'2016, EPFL/Blue Brian Project'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}'
+# The full version, including alpha/beta/rc tags.
+release = '${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+html_title = 'Brain ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR} Python API documentation'
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'BrainPythondoc'
+
+def setup(app):
+    # Connecting a signature processing event to remove the ugly appearance of
+    # some default parameters of C++ wrapped functions
+    # (e.g. (AttributeMap)attributes=<_rtneuron.AttributeMap object at 0x2ac1adb69520>
+    expr = re.compile("<([\.0-9A-Za-z_]*) object at 0x[0-9a-f]*>")
+
+    def remove_cpp_address(app, what, name, obj, options,
+                           signature, return_annotation):
+        if not signature:
+            return (signature, return_annotation)
+
+        def replace(match):
+            return match.group(1) + "()"
+        signature = expr.sub(replace, signature)
+        return (signature, return_annotation)
+
+    def skip_selected(app, what, name, obj, skip, options):
+        # Do not skip constructors
+        if name == "__init__":
+            return False
+        # Skip the 'values' and 'names' attributes from enums
+        if name in ['values', 'names'] and \
+           what == 'class' and type(obj) is dict:
+            return True
+        return skip
+
+    app.connect("autodoc-process-signature", remove_cpp_address)
+    app.connect("autodoc-skip-member", skip_selected)
+
diff --git a/doc/python/index.rst b/doc/python/index.rst
new file mode 100644
index 0000000..b65bc7c
--- /dev/null
+++ b/doc/python/index.rst
@@ -0,0 +1,19 @@
+.. _python-doc:
+
+Brain Python API documentation
+=================================
+
+.. toctree::
+   :maxdepth: 2
+
+brain namespace
+~~~~~~~~~~~~~~~
+.. automodule:: brain._brain
+   :members:
+   :undoc-members:
+
+brain.neuron namespace
+~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: brain._brain._neuron
+   :members:
+   :undoc-members: