This library contains routined to decompress and compress segmentation and to manipulate compressed segmentation data defined by the neuroglancer project.

• Compression and decompression
• (TBD) Interface to relabel and manipulate segmentation from the compressed data
• C++, Python, and Go interface

Compiling as a shared library. Feel free to subsititute e.g. clang for the C++ compiler.

g++ -std=c++11 -O3 -fPIC -shared -I./include src/compress_segmentation.cc src/decompress_segmentation.cc -o compress_segmentation.so

pip Binary Installation

$ pip install compressed-segmentation

$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)

If there are pre-built binaries available this should just work.

pip Source Installation

If you need to build from source, you will need to have a C++ compiler installed and do the following:

$ sudo apt-get install g++ python3-dev 
$ pip install numpy
$ pip install compressed-segmentation

$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)

Direct Installation

Requires a C++ compiler such as g++ or clang.

Works with both Python 2 and 3. Encodes from / decodes to 3D or 4D numpy ndarrays.

$ sudo apt-get install g++ python3-dev 
$ pip install -r requirements.txt
$ python setup.py install

$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)

Please see the licenses in this repo.