.. Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project All rights reserved. This file is part of NeuroM Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. NeuroM Quick-Start ****************** Install ======= Install the latest release: .. code-block:: bash $ pip install neurom Install a specific version: .. code-block:: bash $ pip install neurom==1.2.3 .. note:: It is recommended that you install ``NeuroM`` into a virtualenv. See :ref:`virtualenv setup` for details on how to set that up. .. seealso:: The :ref:`installation instructions` for more details and alternative installation methods. Analyze, visualize, and check ============================= The :py:mod:`neurom` module has various helper functions and command line applications to simplify loading neuron morphologies from files into ``neurom`` data structures and obtaining morphometrics, either from single or multiple neurons. The functionality described here is limited, but it is hoped that it will suffice for most analyses. Extract morphometrics with :py:func:`neurom.get` ------------------------------------------------ These are some of the properties can be obtained for a single neurite type or for all neurites regardless of type via the :py:func:`neurom.get` function: * Segment lengths * Section lengths * Segment radii * Number of sections * Number of sections per neurite * Number of neurites * Number of segments * Local and remote bifurcation angles * Section path distances * Section radial distances * Section branch orders * Total neurite length The usage is simple: .. code:: import neurom as nm nrn = nm.load_neuron('some/data/path/morph_file0.swc') nrn_ap_seg_len = nm.get('segment_lengths', nrn, neurite_type=nm.APICAL_DENDRITE) pop = nm.load_neurons('some/data/path') pop_ap_seg_len = nm.get('segment_lengths', pop, neurite_type=nm.APICAL_DENDRITE) This function also allows obtaining the soma radius and surface area. Iterate over neurites with :py:func:`neurom.iter_neurites` ---------------------------------------------------------- The :py:func:`neurom.iter_neurites` function allows to iterate over the neurites of a sungle neuron or a neuron population. It can also be applied to a single neurite or a list of neurites. It allows to optionally pass a function to be mapped onto each neurite, as well as a neurite filter function. In this example, we apply a simple user defined function to the apical dendrites in a population: .. code:: import neurom as nm def user_func(neurite): print 'Analysinz neurite', neurite return len(neurite.points) stuff = [x for x in nm.iter_neurites(pop, user_func, lambda n : n.type == nm.APICAL_DENDRITE)] .. seealso:: The :py:mod:`neurom` documentation for more details and examples. View neurons with :py:mod:`neurom.viewer` ----------------------------------------- There are also helper functions to plot a neuron in 2 and 3 dimensions. The :py:func:`neurom.viewer.draw` function allows the user to make two and three-dimensional plots of neurites, somata and neurons. It also has a dendrogram neurom plotting mode. .. seealso:: The :py:mod:`neurom.viewer` documentation for more details and examples. Extract morphometrics into JSON files ------------------------------------- The :doc:`morph_stats` application lets you obtain various morphometrics quantities from a set of morphology files. It is highly configurable, and gives access to all the features avaulable via the :py:func:`neurom.get` function. For example, .. code-block:: bash $ morph_stats some/path/morph.swc # single file { "some/path/morph.swc":{ "axon":{ "total_section_length":207.87975220908129, "max_section_length":11.018460736176685, "max_section_branch_order":10, "total_section_volume":276.73857657289523 }, "all":{ "total_section_length":840.68521442251949, "max_section_length":11.758281556059444, "max_section_branch_order":10, "total_section_volume":1104.9077419665782 }, "mean_soma_radius":0.17071067811865476, "apical_dendrite":{ "total_section_length":214.37304577550353, "max_section_length":11.758281556059444, "max_section_branch_order":10, "total_section_volume":271.9412385728449 }, "basal_dendrite":{ "total_section_length":418.43241643793476, "max_section_length":11.652508126101711, "max_section_branch_order":10, "total_section_volume":556.22792682083821 } } } $ morph_stats some/path # all files in directory .. seealso:: The :doc:`morph_stats documentation page` Check data validity ------------------- The :doc:`morph_check` application applies some structural and semantic checks to morphology data files in order to determine whether it is suitable to construct a neuron structure and whether certain defects within the structure are detected. It can be invoked from the command line, and takes as main argument the path to either a single file or a directory of morphology files. For example, .. code-block:: bash $ morph_check some/path/morph.swc # single file INFO: ======================================== INFO: File: test_data/swc/Neuron.swc INFO: Is single tree PASS INFO: Has soma points PASS INFO: No missing parents PASS INFO: Has sequential ids PASS INFO: Has increasing ids PASS INFO: Has valid soma PASS INFO: Has valid neurites PASS INFO: Has basal dendrite PASS INFO: Has axon PASS INFO: Has apical dendrite PASS INFO: Has all nonzero segment lengths PASS INFO: Has all nonzero section lengths PASS INFO: Has all nonzero neurite radii PASS INFO: Has nonzero soma radius PASS INFO: ALL PASS INFO: ======================================== $ morph_check test_data/swc # all files in directory # loops over all morphology files found in test_data/swc .. seealso:: The :doc:`morph_check documentation page`