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PATATO

PATATO: a Python photoacoustic tomography analysis toolkit - Published in JOSS (2024)

https://github.com/bohndieklab/patato

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Mathematics Computer Science - 84% confidence
Artificial Intelligence and Machine Learning Computer Science - 83% confidence
Earth and Environmental Sciences Physical Sciences - 62% confidence
Last synced: 4 months ago · JSON representation

Repository

PATATO: A Python PhotoAcoustic Tomography Analysis Toolkit

Basic Info
  • Host: GitHub
  • Owner: BohndiekLab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 60 MB
Statistics
  • Stars: 20
  • Watchers: 1
  • Forks: 6
  • Open Issues: 7
  • Releases: 18
Created over 2 years ago · Last pushed 4 months ago
Metadata Files
Readme Contributing License

README.md

Journal of open source software status Documentation Status License: MIT PyPI version Build

Logo

PATATO: PhotoAcoustic Tomography Analysis TOolkit

Documentation

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 (telse@ic.ac.uk).

Getting Started

In order to use PATATO, you must have a Python environment set up on your computer. We recommend using uv (https://docs.astral.sh/uv/) to run Python. This will help you to avoid dependency conflicts. You can alternatively use Anaconda or virtual environments.

We currently recommend running PATATO on Python version 3.12.

You can install patato with uv like so:

shell uv add patato

Or, using pip:

shell pip install patato

To setup support for GPU-based reconstruction, 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.

Documentation, examples and contributing

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

Copyright (c) Thomas Else 2022-25. Distributed under a MIT License.

Owner

  • Name: VISIONLAB at the University of Cambridge
  • Login: BohndiekLab
  • Kind: organization

JOSS Publication

PATATO: a Python photoacoustic tomography analysis toolkit
Published
January 19, 2024
DOI
Volume 9, Issue 93, Page 5686
Authors
Thomas R. Else ORCID
CRUK Cambridge Institute, University of Cambridge, United Kingdom, Department of Physics, University of Cambridge, United Kingdom
Janek Gröhl ORCID
CRUK Cambridge Institute, University of Cambridge, United Kingdom, Department of Physics, University of Cambridge, United Kingdom
Lina Hacker ORCID
CRUK Cambridge Institute, University of Cambridge, United Kingdom, Department of Physics, University of Cambridge, United Kingdom, Department of Oncology, University of Oxford, United Kingdom
Sarah E. Bohndiek ORCID
CRUK Cambridge Institute, University of Cambridge, United Kingdom, Department of Physics, University of Cambridge, United Kingdom
Editor
Aoife Hughes ORCID
Tags
Photoacoustics Imaging Optoacoustics MSOT Reconstruction Backprojection Unmixing
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 1
  • Watch event: 7
  • Delete event: 2
  • Push event: 11
  • Pull request review comment event: 1
  • Pull request event: 6
  • Create event: 3
Last Year
  • Issues event: 1
  • Watch event: 7
  • Delete event: 2
  • Push event: 11
  • Pull request review comment event: 1
  • Pull request event: 6
  • Create event: 3

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 380
  • Total Committers: 3
  • Avg Commits per committer: 126.667
  • Development Distribution Score (DDS): 0.126
Past Year
  • Commits: 26
  • Committers: 3
  • Avg Commits per committer: 8.667
  • Development Distribution Score (DDS): 0.115
Top Committers
Name Email Commits
Thomas Else 5****e 332
Thomas Else t****e@c****k 44
Janek Grohl j****l@c****k 4
Committer Domains (Top 20 + Academic)
cruk.cam.ac.uk: 2

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 11
  • Total pull requests: 59
  • Average time to close issues: 3 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 5
  • Total pull request authors: 5
  • Average comments per issue: 2.55
  • Average comments per pull request: 0.12
  • Merged pull requests: 51
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 2
  • Pull requests: 13
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Issue authors: 1
  • Pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.54
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • tomelse (4)
  • MengjieSHI (3)
  • ASK-DataScience (2)
  • anirbanchakraborty96 (1)
  • frisograce (1)
Pull Request Authors
  • tomelse (65)
  • jgroehl (3)
  • dependabot[bot] (2)
  • ij264 (1)
  • Mo-Sc (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels
dependencies (2) github_actions (2) enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 4,057 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 29
  • Total maintainers: 1
pypi.org: patato

A Python Toolkit for the analysis of photoacoustic tomography data.

  • Homepage: https://github.com/bohndieklab/patato
  • Documentation: https://patato.readthedocs.io
  • 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.
  • Latest release: 0.6.1
    published 4 months ago
  • Versions: 29
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 4,057 Last month
Rankings
Downloads: 5.1%
Dependent packages count: 10.1%
Average: 16.9%
Dependent repos count: 21.6%
Forks count: 22.6%
Stargazers count: 25.0%
Maintainers (1)
thomaselse
Last synced: 4 months ago

Dependencies

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requirements.txt pypi
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setup.py pypi