A Python Toolkit for the analysis of photoacoustic tomography data.

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Project description

PATATO: PhotoAcoustic Tomography Analysis TOolkit

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.

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.

Documentation, examples and contributing

Documentation for PATATO can be found at https://patato.readthedocs.io/en/latest/?badge=latest.

Project details

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Release history Release notifications | RSS feed

0.6.0

Sep 11, 2024

0.5.17

Sep 11, 2024

0.5.16

Jul 16, 2024

0.5.15

Jul 2, 2024

0.5.14

Dec 4, 2023

0.5.13

Dec 4, 2023

0.5.12

Sep 27, 2023

0.5.11

Sep 26, 2023

0.5.10

Sep 18, 2023

0.5.8

Aug 16, 2023

0.5.7

Aug 2, 2023

0.5.5

Jul 21, 2023

0.5.2

Jun 28, 2023

0.5.1 yanked

Jun 24, 2023

Reason this release was yanked:

Doesn't correctly load the spectra/presets etc.

0.5.0

Jun 14, 2023

0.4.0

May 12, 2023

0.2.4

Apr 4, 2023

0.2.3

Feb 28, 2023

This version

0.2.2

Feb 27, 2023

0.2.1

Jan 30, 2023

0.2.0

Jan 23, 2023

0.1.4

Jan 20, 2023

0.1.3

Jan 19, 2023

0.1.2

Jan 19, 2023

0.1.1

Jan 17, 2023

0.1.0

Jan 12, 2023

0.0.2

Jan 12, 2023

0.0.1

Jan 11, 2023

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patato 0.2.2

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PATATO: PhotoAcoustic Tomography Analysis TOolkit

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