Commit 426c5e40 authored by Philipp Schubert's avatar Philipp Schubert
Browse files

updates in environment.yml, README.md and setup.py

parent a812ed66
Pipeline #115535 passed with stage
in 2 minutes and 4 seconds
......@@ -4,30 +4,28 @@
[![coverage report](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/badges/master/coverage.svg)](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/commits/master)
[![pylint status](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/-/jobs/artifacts/master/raw/pylint/pylint.svg?job=pylint)](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/-/jobs/artifacts/master/raw/pylint/pylint.log?job=pylint)
SyConn
SyConn2
------
Refactored version of SyConn for automated synaptic connectivity inference based on dense EM segmentation data. For the first version
see below or checkout the branch [dorkenwald2017nm](https://github.com/StructuralNeurobiologyLab/SyConn/tree/dorkenwald2017nm).
Connectomic analysis toolkit for automated synaptic connectivity inference based on dense EM segmentation data.
Current features:
- introduction of classes for handling of supervoxels (e.g. cell fragments, predicted cellular
organelles like mitochondria, vesicle clouds etc.) and agglomerated supervoxels
- distributed prediction of sub-cellular structures, supervoxel extraction and mesh
generation
- (sub-) cellular compartment (spines, bouton and axon/dendrite/soma) and cell type classification with multiview- [\[2\]](https://www.nature.com/articles/s41467-019-10836-3) and with skeleton-based approaches [\[1\]](https://www.nature.com/articles/nmeth.4206)
- glia identification and separation [\[2\]](https://www.nature.com/articles/s41467-019-10836-3)
- connectivity matrix export
- KNOSSOS plugin for interactive exploration (work in progress)
- interface to supervoxel properties for various types (e.g. cell fragments, synapses, mitochondria, vesicle clouds, ..) and entire cell reconstructions
(associated cell objects, mesh, skeleton, prediction results, ..)
- (sub-) cellular compartment (spines, boutons and axon/dendrite/soma) and cell type classification with multiview- [\[2\]](https://www.nature.com/articles/s41467-019-10836-3) and with skeleton-based approaches [\[1\]](https://www.nature.com/articles/nmeth.4206)
- distributed parallelization (SLURM, QSUB) of all processing steps
- astrocyte identification and separation [\[2\]](https://www.nature.com/articles/s41467-019-10836-3)
- neuroglancer web interface
If you use parts of this code base in your academic projects, please cite the corresponding publication(s).
To access v1 of SyConn
please checkout the branch [dorkenwald2017nm](https://github.com/StructuralNeurobiologyLab/SyConn/tree/dorkenwald2017nm) or have a look at
the [documentation](https://structuralneurobiologylab.github.io/SyConn/documentation/).
We also present more general information about SyConn on our [Website](https://structuralneurobiologylab.github.io/SyConn/).
Documentation
-------------
The documentation for the refactored version is still work-in-progress and can be found [here](docs/doc.md). Alternatively and for API docs please refer to the latest [readthedocs build](https://syconn.readthedocs.io/en/latest/).
For SyConn v1, please refer to the old [documentation](https://structuralneurobiologylab.github.io/SyConn/documentation/). We also present more general information about SyConn on our [Website](https://structuralneurobiologylab.github.io/SyConn/).
The documentation including API docs can be found as [readthedocs build](https://syconn.readthedocs.io/en/latest/) or partially as markdown [here](docs/doc.md).
The Team
--------
......
......@@ -79,19 +79,19 @@ dependencies:
- plyfile
# Pre-release packages
- git+https://github.com/ELEKTRONN/elektronn3.git@syconn#egg=elektronn3
- git+https://github.com/knossos-project/knossos_utils.git@dev#egg=knossos_utils
- git+https://github.com/StructuralNeurobiologyLab/MorphX.git@master#egg=morphx
# training scripts
- git+https://github.com/StructuralNeurobiologyLab/NeuronX.git
- git+https://github.com/ELEKTRONN/elektronn3.git@syconn2#egg=elektronn3
- git+https://github.com/knossos-project/knossos_utils.git@syconn2#egg=knossos_utils
- git+https://github.com/StructuralNeurobiologyLab/MorphX.git@v0.1#egg=MorphX
# cloud-volume >=4 throws an error in simple_merge during np.concatenate if any skeleton has no vertices
- git+https://github.com/StructuralNeurobiologyLab/kimimaro.git
# point models
# point models
- git+https://github.com/StructuralNeurobiologyLab/LightConvPoint.git
# # training scripts
# - git+https://github.com/StructuralNeurobiologyLab/NeuronX.git
#for skeletonisation
- fill-voids
......@@ -17,7 +17,7 @@ except ImportError as e:
print("WARNING: Could not build cython modules. {}".format(e))
cython_out = None
VERSION = '0.3'
VERSION = '2.0'
def read_readme():
......
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