| Name | patato JSON |
| Version |
0.6.0
JSON |
| download |
| home_page | None |
| Summary | A Python Toolkit for the analysis of photoacoustic tomography data. |
| upload_time | 2024-09-11 22:32:03 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | <3.13,>=3.8 |
| license | MIT License Copyright (c) 2023 Thomas Else Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
photoacoustics
jax
tomography
reconstruction
spectral unmixing
dynamic contrast enhanced
backprojection
model based
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7)
[](https://patato.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/bohndieklab/patato/blob/main/LICENSE.MD)
[](https://badge.fury.io/py/patato)
[](https://github.com/bohndieklab/patato/actions/workflows/build_wheels.yml)
# PATATO: PhotoAcoustic Tomography Analysis TOolkit
[Documentation](https://patato.readthedocs.io/en/develop/)
PATATO is an Open-Source project to enable the analysis of photoacoustic (PA) imaging data in a transparent, reproducible and extendable way. We provide efficient, GPU-optimised implementations of common PA algorithms written around standard Python libraries, including filtered backprojection, model-based reconstruction and spectral unmixing.
The tool supports many file formats, such as the International Photoacoustic Standardisation Consortium (IPASC) data format, and it can be extended to support custom data formats. We hope that this toolkit can enable faster and wider dissemination of analysis techniques for PA imaging and provide a useful tool to the community.
* Please report any bugs or issues you find to our GitHub repository
* Please do get involved! Contact Thomas Else (thomas.else@cruk.cam.ac.uk).
## Getting Started
In order to use PATATO, you must have a Python environment set up on your computer. We recommend using Anaconda (http://anaconda.com) to run Python, particularly if you are using Windows. You may wish to setup a separate Anaconda environment to install PATATO to minimise conflicts between dependency versions.
```shell
pip install --upgrade pip setuptools
pip install patato
```
To setup support for image reconstruction on Windows, or for GPU support, please follow the installation guide in the documentation.
## Citing PATATO
To cite PATATO, please reference our article in the Journal of Open Source software, [here](https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7).
## Documentation, examples and contributing
Documentation for PATATO can be found at https://patato.readthedocs.io/en/latest/?badge=latest.
Copyright (c) Thomas Else 2022-23.
Distributed under a MIT License.
Raw data
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