PlatiPy

PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python - Published in JOSS (2023)

https://github.com/pyplati/platipy

Science Score: 100.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 8 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org
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Committers with academic emails
1 of 12 committers (8.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

image-analysis medical-imaging python registration segmentation visualization

Keywords from Contributors

mesh

Scientific Fields

Computer Science Computer Science - 88% confidence

Artificial Intelligence and Machine Learning Computer Science - 83% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Processing Library and Analysis Toolkit for Medical Imaging in Python

Basic Info

Host: GitHub
Owner: pyplati
License: apache-2.0
Language: Python
Default Branch: master
Homepage: https://pyplati.github.io/platipy/
Size: 199 MB

Statistics

Stars: 135
Watchers: 3
Forks: 29
Open Issues: 30
Releases: 15

Topics

image-analysis medical-imaging python registration segmentation visualization

Created over 5 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing Citation

PlatiPy

Processing Library and Analysis Toolkit for Medical Imaging in Python

PlatiPy is a library of amazing tools for image processing and analysis - designed specifically for medical imaging!

Check out the PlatiPy documentation for more info.

This project was motivated by the need for a simple way to use, visualise, process, and analyse medical images. Many of the tools and algorithms are designed in the context of radiation therapy, although they are more widely applicable to other fields that use 2D, 3D, or 4D imaging.

PlatiPy is written in Python, and uses SimpleITK, VTK, and standard Python libraries. Jupyter notebooks are provided where possible, mainly for guidance on getting started with using the tools. We welcome feedback and contributions from the community (yes, you!) and you can find more information about contributing here.

What can I do with platipy?

A lot! A good place to start is by looking in the examples directory.

Or checkout this presentation by Rob Finnegan at MRI Together 2023 for a great overview of PlatiPy:

Some examples of what PlatiPy can do:

DICOM organising and converting:
- Bulk convert from multiple series and studies with a single function
- Convert DICOM-RT structure and dose files to NIfTI images
- Create DICOM-RT structure files from binary masks e.g. from automatic contouring algorithms
Image registration
- Register images and transform labels with a few lines of code
- Linear transformations: rigid, affine, similarity
- Non-linear deformable transformations: demons, b-splines
- Multiple metrics for optimisation
Atlas-based segmentation
- A suite of tools that can be used out-of-the-box
- Includes advanced algorithms for iterative atlas selection and vessel splining
Synthetic deformation field generation
- Simulate anatomically realistic shifts, expansions, and bending
- Compare DIR results from clinical systems
Basic tools for image processing and analysis
- Computing label similarity metrics: DSC, mean distance to agreement, Hausdorff distance, and more
- Cropping images to a region of interest
- Rotate images and generate maximum/mean intensity projections (beams eye view modelling)

A major part of this package is visualisation, and some examples are shown below!

Visualise some contours

``` python from platipy.imaging import ImageVisualiser

vis = ImageVisualiser(image) vis.add_contour(contours) fig = vis.show() ```

Register some images

```python from platipy.imaging.registration.linear import linear_registration

image2registered, tfm = linearregistration( image1, image_2 )

vis = ImageVisualiser(image1) vis.addcomparisonoverlay(image2_registered) fig = vis.show() ```

Calculate deformation vector fields

```python from platipy.imaging.registration.deformable import fastsymmetricforcesdemonsregistration

image2deformed, tfmdir, dvf = fastsymmetricforcesdemonsregistration( image1, image2registered )

vis = ImageVisualiser(image2deformed, axis="z") vis.addvectoroverlay( dvf, subsample=12, arrowscale=1, arrowwidth=2, colormap=plt.cm.magma, name="DVF magnitude [mm]", color_function="magnitude" ) fig = vis.show() ```

Getting started

There aren't many requirements, just an installed Python interpreter (3.7 or greater). PlatiPy can be installed with pip:

bash pip install platipy

The base installation of platipy does not include some large libraries needed for various components of platipy. The following extras are available to install to run specific platipy tools:

bash pip install platipy[cardiac] pip install platipy[nnunet] pip install platipy[backend]

Authors

Phillip Chlap - phillip.chlap@unsw.edu.au
Robert Finnegan - robert.finnegan@sydney.edu.au

Owner

Name: pyplati
Login: pyplati
Kind: organization

Repositories: 1
Profile: https://github.com/pyplati

JOSS Publication

PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python

Published

June 26, 2023

DOI

10.21105/joss.05374

Volume 8, Issue 86, Page 5374

Authors

Phillip Chlap

South Western Sydney Clinical School, University of New South Wales, Australia, Ingham Institute for Applied Medical Research, Australia, Liverpool Cancer Therapy Centre, Liverpool Hospital, Australia

Robert N. Finnegan

University of Sydney, Australia, Ingham Institute for Applied Medical Research, Australia, Northern Sydney Cancer Centre, Royal North Shore Hospital, Australia

Editor

Samuel Forbes

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Chlap
  given-names: Phillip
  orcid: "https://orcid.org/0000-0002-6517-8745"
- family-names: Finnegan
  given-names: Robert N.
  orcid: "https://orcid.org/0000-0003-4728-8462"
doi: 10.5281/zenodo.8032858
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Chlap
    given-names: Phillip
    orcid: "https://orcid.org/0000-0002-6517-8745"
  - family-names: Finnegan
    given-names: Robert N.
    orcid: "https://orcid.org/0000-0003-4728-8462"
  date-published: 2023-06-26
  doi: 10.21105/joss.05374
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5374
  title: "PlatiPy: Processing Library and Analysis Toolkit for Medical
    Imaging in Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05374"
  volume: 8
title: "PlatiPy: Processing Library and Analysis Toolkit for Medical
  Imaging in Python"

GitHub Events

Total

Issues event: 9
Watch event: 19
Delete event: 2
Issue comment event: 17
Push event: 4
Pull request review event: 4
Pull request event: 11
Fork event: 2
Create event: 5

Last Year

Issues event: 9
Watch event: 19
Delete event: 2
Issue comment event: 17
Push event: 4
Pull request review event: 4
Pull request event: 11
Fork event: 2
Create event: 5

Committers

Last synced: 5 months ago

All Time

Total Commits: 744
Total Committers: 12
Avg Commits per committer: 62.0
Development Distribution Score (DDS): 0.402

Past Year

Commits: 10
Committers: 4
Avg Commits per committer: 2.5
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Phillip Chlap	p**p@u**u	445
rnfinnegan	r**n@g**m	240
dependabot[bot]	4****]	41
Simon Biggs	s**s@r**i	8
Phillip Chlap	p**p@s**u	3
S. Gay	s**7@g**m	1
Justin Kirby	2****u	1
Jing Zhang	j**r@g**m	1
Gabriele	g**b@g**m	1
David Barbee	b**d@g**m	1
Daniel Al Mouiee	d**e@g**m	1
Phillip Chlap	p**p@r**m	1

Committer Domains (Top 20 + Academic)

radformation.com: 1 sirob.eu: 1 radiotherapy.ai: 1 unsw.edu.au: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 48
Total pull requests: 72
Average time to close issues: about 1 year
Average time to close pull requests: 25 days
Total issue authors: 31
Total pull request authors: 9
Average comments per issue: 2.13
Average comments per pull request: 0.17
Merged pull requests: 60
Bot issues: 0
Bot pull requests: 38

Past Year

Issues: 10
Pull requests: 14
Average time to close issues: 5 days
Average time to close pull requests: 2 days
Issue authors: 9
Pull request authors: 4
Average comments per issue: 1.2
Average comments per pull request: 0.21
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 7

View more stats

Top Authors

Issue Authors

pchlap (5)
dalmouiee (5)
rnfinnegan (5)
MarkGardnerUSyd (3)
Ken32g (2)
CrytoGen (2)
denbonte (2)
jaketakes (1)
1413194910 (1)
bwheelz36 (1)
YYAN97 (1)
brendan-whelan-seetreat (1)
dlbarbee (1)
MLK97 (1)
VincentBourbon (1)

Pull Request Authors

dependabot[bot] (61)
pchlap (30)
rnfinnegan (3)
kirbyju (2)
dlbarbee (2)
dalmouiee (2)
jizhang02 (2)
tomaroberts (2)
StellarStorm (1)

Top Labels

Issue Labels

Pull Request Labels

dependencies (61) python (7)

Packages

Total packages: 1
Total downloads:
- pypi 1,125 last-month
Total docker downloads: 674

Total dependent packages: 3
Total dependent repositories: 9
Total versions: 20
Total maintainers: 1

pypi.org: platipy

Processing Library and Analysis Toolkit for Medical Imaging in Python

Documentation: https://platipy.readthedocs.io/
License: Apache 2.0 License
Latest release: 0.7.2
published over 1 year ago

Versions: 20
Dependent Packages: 3
Dependent Repositories: 9
Downloads: 1,125 Last month
Docker Downloads: 674

Rankings

Docker downloads count: 2.0%

Dependent packages count: 2.4%

Average: 4.3%

Dependent repos count: 4.9%

Downloads: 7.8%

Maintainers (1)

phillip.chlap

Last synced: 4 months ago

Dependencies

services/nnunet/requirements-nnunet.txt pypi

torch *
torchaudio *
torchvision *

services/radiomics/requirements-radiomics.txt pypi

pyradiomics ==3.0.1

.github/workflows/build_docs.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
peaceiris/actions-gh-pages v3 composite

.github/workflows/package.yml actions

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docker/build-push-action v2 composite
docker/login-action v1 composite
docker/setup-buildx-action v1 composite
docker/setup-qemu-action v1 composite

.github/workflows/pull_request.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/release.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
peaceiris/actions-gh-pages v3 composite
peter-evans/repository-dispatch v1 composite

Dockerfile docker

ubuntu 20.04 build

docker-compose.yml docker

platipy/platipy dev
redis latest

services/bronchus/Dockerfile docker

platipy/platipy service build

services/cardiac/Dockerfile docker

platipy/platipy service build

services/dirqa/Dockerfile docker

platipy/platipy service build

services/jupyter/Dockerfile docker

platipy/platipy latest build

services/jupyter/docker-compose.yml docker

platipy/platipy jupyter

services/mridixon/Dockerfile docker

platipy/platipy service build

services/nnunet/Dockerfile docker

platipy/platipy service build

services/pinnacle/Dockerfile docker

platipy/platipy service build

services/radiomics/Dockerfile docker

platipy/platipy service build

services/sample/Dockerfile docker

platipy/platipy service build

poetry.lock pypi

202 dependencies

pyproject.toml pypi

Flask ^2.1.0
Flask-RESTful >=0.3.8
Flask-SQLAlchemy ^2.4.4
Jinja2 ^3.1
SimpleITK ^2.0.2
celery ^5.2.3
click ^8.0.3
gunicorn ^20.0.4
matplotlib ^3.2.2
nnunet ^1.7.0
pandas ^1.3.0
psutil ^5.8.0
pydicom ^2.1.2
pymedphys >=0.38.0
pynetdicom ^2.0.2
python ^3.8.0
redis ^3.5.3
requests ^2.25.1
rt-utils ^1.1.4
scikit-image >=0.18.1
vtk ^9.1.0

services/totalsegmentator/Dockerfile docker

nvidia/cuda 12.2.0-runtime-ubuntu22.04 build

services/dirqa/requirements-dirqa.txt pypi

services/totalsegmentator/requirements-totalseg.txt pypi

TotalSegmentator *
torch *
torchaudio *
torchvision *

PlatiPy

Science Score: 100.0%

Keywords

Keywords from Contributors

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

PlatiPy

Processing Library and Analysis Toolkit for Medical Imaging in Python

What can I do with platipy?

Visualise some contours

Register some images

Calculate deformation vector fields

Getting started

Authors

Owner

JOSS Publication

PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

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Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: platipy

Rankings

Maintainers (1)

Dependencies