Commit d0cbec94 authored by Philipp Schubert's avatar Philipp Schubert
Browse files

minor channges in docs

parent 1c126bd8
build:
image: latest
image: latest
python:
pip_install: true
version: 3.6
conda:
file: environment.yml
pip_install: false
version: 3.5
conda:
file: environment.yml
requirements_file: requirements.txt
formats: []
\ No newline at end of file
[![Documentation Status](https://readthedocs.org/projects/syconn/badge/?version=latest)](https://syconn.readthedocs.io/en/latest/?badge=latest)
# SyConn v2
# SyConn
Refactored (still an early stage construction) version of SyConn for automated synaptic connectivity inference based on dense EM segmentation data.
For v0.1 see the SyConn branch [dorkenwald2017nm](https://github.com/StructuralNeurobiologyLab/SyConn/tree/dorkenwald2017nm).
Version 0.2 currently features:
v0.2 currently features:
- introduction of supervoxel and agglomerated supervoxel classes
- added support for (sub-) cellular compartment (spines, axon/dendrite/soma) and cell type classification with [skeleton](https://www.nature.com/articles/nmeth.4206)- and [multiview-based](https://www.biorxiv.org/content/early/2018/07/06/364034) approaches
- cell organelle prediction, extraction and mesh generation
......@@ -14,8 +14,9 @@ Version 0.2 currently features:
## System requirements & installation
* Python 3.5
* The whole pipeline was designed and tested on Linux systems (CentOS, Arch)
* SyConn is based on the packages [elektronn](http://elektronn.org), [knossos-utils](https://github.com/knossos-project/knossos_utils)
is used for visualization and annotation of 3D EM data sets.
* SyConn is primarily based on the packages [elektronn](http://elektronn.org) and [knossos-utils](https://github.com/knossos-project/knossos_utils)
* We use [KNOSSOS](https://knossostool.org/)
for visualization and annotation of 3D EM data sets.
* [VIGRA](https://ukoethe.github.io/vigra/), e.g. ``conda install -c ukoethe vigra``
* osmesa, e.g.: ``conda install -c menpo osmesa``
......@@ -28,7 +29,7 @@ You can install SyConn using ``git`` and ``pip``:
## Tutorials & documentation
For the SyConn documentation see [here](docs/doc.md) or check out the latest readthedocs build [here](https://syconn.readthedocs.io/en/latest/). Alternatively you can build the API documentation lcoally by running `make html` in the `docs` folder.
For the SyConn documentation see [here](docs/doc.md) or check out the latest readthedocs build [here](https://syconn.readthedocs.io/en/latest/). Alternatively you can build the API documentation locally by running `make html` in the `docs` folder.
# The Team
The Synaptic connectivity inference toolkit is developed at Max-Planck-Institute of Neurobiology, Munich.
......
......@@ -36,6 +36,7 @@ extensions = [
'sphinx.ext.githubpages',
'sphinx.ext.napoleon',
'sphinx.ext.viewcode',
'sphinx_autodoc_typehints',
'm2r',
]
......@@ -61,8 +62,8 @@ master_doc = 'index'
# General information about the project.
project = u'SyConn'
copyright = u'2016, Sven Dorkenwald, Philipp Schubert, Jörgen Kornfeld'
author = u'Sven Dorkenwald, Philipp Schubert, Jörgen Kornfeld'
copyright = u'2018, SyConn team'
author = u'Philipp Schubert, Sven Dorkenwald, Jörgen Kornfeld'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
......@@ -138,9 +139,8 @@ html_theme = 'sphinxdoc'
# documentation.
#
# html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
# html_theme_path = []
# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
# The name for this set of Sphinx documents.
# "<project> v<release> documentation" by default.
......@@ -165,7 +165,7 @@ html_theme = 'sphinxdoc'
# 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', 'images']
html_static_path = ['_static']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
......
......@@ -25,7 +25,7 @@ API
syconn
Indices and tables
==================
------------------
:ref:`genindex`
:ref:`modindex`
......
syconn package
==============
syconn API
==========
Subpackages
-----------
......
......@@ -28,5 +28,4 @@ dependencies:
# For docs:
- sphinx >=1.7.5
- sphinx_rtd_theme >=0.4.0
- sphinx-autodoc-typehints >=1.3.0
\ No newline at end of file
......@@ -24,7 +24,8 @@ config = {
'numpy', 'scipy', 'lz4', 'h5py', 'networkx', 'numba',
'configobj', 'fasteners', 'flask', 'coloredlogs',
'opencv-python', 'pyopengl', 'scikit-learn',
'scikit-image', 'm2r'],
'scikit-image', 'm2r',
'sphinx-autodoc-typehints'],
'name': 'SyConn',
'dependency_links': ['https://github.com/knossos-project/knossos_utils'
'/tarball/master#egg=knossos_utils',
......
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