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Neuroglancer compressed_segmentation codec.

Project description

NOTE: This repository is the PyPI distribution repo but is based on work done by Jeremy Maitin-Shepard (Google), Stephen Plaza (Janelia Research Campus), and William Silversmith (Princeton) here: https://github.com/janelia-flyem/compressedseg

# Compress Seg [![Picture](https://raw.github.com/janelia-flyem/janelia-flyem.github.com/master/images/HHMI_Janelia_Color_Alternate_180x40.png)](http://www.janelia.org)
## Library for compressing and decompressing image segmentation (adapted from [neuroglancer](https://github.com/google/neuroglancer))

This library contains routined to decompress and compress segmentation and to manipulate compressed segmentation data defined by the [neuroglancer project](https://github.com/google/neuroglancer/blob/master/src/neuroglancer/sliceview/compressed_segmentation/README.md).

### Features

* Compression and decompression
* (TBD) Interface to relabel and manipulate segmentation from the compressed data
* C++, Python, and Go interface (see original repo for Golang)

### C++ Compilation

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

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

### Python 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.

```bash
$ pip install -r requirements.txt
$ python setup.py install

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

### License

Please see the licenses in this repo.

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