Tomographic reconstruction software for PET, PET-MRI and SPECT in 2D, 3D (volumetric) and 4D (spatio-temporal) in Python.
The software provides high-speed reconstruction using Graphics Processing Units (GPU). Note: an NVidia CUDA compatible GPU is required.
Occiput can be utilized with arbitrary scanner geometries. It provides production quality image reconstruction with standard algorithms (such as MLEM and OSEM) and implements advanced algorithms for motion correction, kinetic imaging and for multi-modal reconstruction.
The source code contains Jupyter notebooks with examples.
A Python package implementing the interface to the Siemens Biograph mMR PET-MRI scanner is available upon request and following authorization from Siemens. Please email us at occiput.reconstruction@gmail.com
Installation
Linux, Windows (not tested recently), MacOS
Pre-requisites: Occiput requires NVidia GPU Drivers`, ``NVidia CUDA and the NiftyRec GPU accelerated tomographic ray-tracing library.
Make sure that CUDA libraries and NiftyRec libraries are in the system path:
Linux:
export LD_LIBRARY_PATH:$LD_LIBRARY_PATH:/path_to_cuda_libraries:/path_to_niftyrec_libraries
MacOS:
export DYLD_LIBRARY_PATH:$DYLD_LIBRARY_PATH:/path_to_cuda_libraries:/path_to_niftyrec_libraries
Windows:
setx path “%path%;c:/path_to_cuda_libraries:/path_to_niftyrec_libraries;”
Install Occiput:
git clone https://github.com/spedemon/occiput.git
python setup.py build install
Getting started
Examples and demos of the features of Occiput are in the /occiput/notebooks folder. To get started, install Python Jupyter and open the scripts in /occiput/notebooks
Website
For more information see occiput.io.
1 maintainer
Metadata
1 maintainer
Release files for occiput 1.0.12
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| occiput-1.0.12.tar.gz | 2.4 MB | Details |
Release files / occiput-1.0.12.tar.gz
| Download URL | occiput-1.0.12.tar.gz |
|---|---|
| Size | 2.4 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
95eed499880a5e4aa815ed930ed95f72ded8d9537faac2baf0b1eadf08bf0376
|
|
BLAKE2b-256 checksum How to use checksums |
a0edbf2e4836ed9c8cccba92a29a7a3fe31d12a9f364299866e4d2884bfdadc7
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
