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labelfusion

Implementation of various label fusion approaches for medical imaging.

https://github.com/fets-ai/labelfusion

Science Score: 77.0%

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
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 15 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

fusion itk label-fusion label-fusion-approaches labels medical segmentation simpleitk
Last synced: 6 months ago · JSON representation ·

Repository

Implementation of various label fusion approaches for medical imaging.

Basic Info
  • Host: GitHub
  • Owner: FeTS-AI
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage: https://www.fets.ai
  • Size: 408 KB
Statistics
  • Stars: 14
  • Watchers: 1
  • Forks: 6
  • Open Issues: 2
  • Releases: 11
Topics
fusion itk label-fusion label-fusion-approaches labels medical segmentation simpleitk
Created about 5 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

LabelFusion

Build Status DOI

This repo contains implementation of various label fusion approaches that can be used to fuse multiple labels.

Installation

Default

sh conda create -n venv_labelFusion python=3.12 -y conda activate venv_labelFusion pip install LabelFusion

For Development

```sh

fork to your own repo

git clone ${yourForklabelFusionrepo_link} cd LabelFusion conda create -p ./venv python=3.12 -y conda activate ./venv pip install -e .

develop, push

initiate pull request

```

Available fusion methods:

Usage

Command-Line interface

```sh

continue from previous shell

python fusion_run -h -h, --help show this help message and exit -inputs INPUTS The absolute, comma-separated paths of labels that need to be fused -classes CLASSES The expected labels; for example, for BraTS, this should be '0,1,2,3' - not used for STAPLE or ITKVoting -method METHOD The method to apply; currently available: STAPLE | ITKVoting | MajorityVoting | SIMPLE -output OUTPUT The output file to write the results ```

Example: ```sh

continue from previous shell

python fusionrun \ -inputs /path/to/segalgo0.nii.gz,/path/to/segalgo1.nii.gz,/path/to/segalgo2.nii.gz \ -classes 0,1,2,3 \ -method STAPLE \ -output /path/to/segfusion.nii.gz ```

Python interface

```python

assuming virtual environment containing LabelFusion is activated

import SimpleITK as sitk from LabelFusion.wrapper import fuse_images

labeltofuse0 = '/path/to/segalgo0.nii.gz' labeltofuse1 = '/path/to/segalgo1.nii.gz'

imagestofuse = [] imagestofuse.append(sitk.ReadImage(labeltofuse0, sitk.sitkUInt8)) imagestofuse.append(sitk.ReadImage(labeltofuse1, sitk.sitkUInt8)) fusedstaple = fuseimages(imagestofuse, 'staple') # classlist is not needed for staple/itkvoting sitk.WriteImage(fusedstaple, '/path/to/outputstaple.nii.gz') fusedsimple = fuseimages(imagestofuse, 'simple', classlist=[0,1,2,3]) sitk.WriteImage(fusedsimple, '/path/to/outputsimple.nii.gz') ```

Testing

This repo has continuous integration enabled via GitHub Actions for the following operating systems:

  • Windows
  • Ubuntu
  • macOS

And for the following python versions:

  • 3.9
  • 3.10
  • 3.11
  • 3.12

Owner

  • Name: Federated Tumor Segmentation (FeTS) initiative
  • Login: FETS-AI
  • Kind: organization
  • Email: admin@fets.ai
  • Location: Philadelphia, PA

Federated Learning in medicine

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Pati"
  given-names: "Sarthak"
  orcid: "https://orcid.org/0000-0003-2243-8487"
- family-names: "Bakas"
  given-names: "Spyridon"
  orcid: "https://orcid.org/0000-0001-8734-6482"
title: "LabelFusion"
version: 1.0.11
doi: 10.5281/zenodo.4633206
date-released: 2021-03-24
url: "https://github.com/CBICA/LabelFusion"

GitHub Events

Total
  • Release event: 1
  • Push event: 9
  • Pull request event: 2
Last Year
  • Release event: 1
  • Push event: 9
  • Pull request event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 206
  • Total Committers: 3
  • Avg Commits per committer: 68.667
  • Development Distribution Score (DDS): 0.058
Past Year
  • Commits: 14
  • Committers: 3
  • Avg Commits per committer: 4.667
  • Development Distribution Score (DDS): 0.429
Top Committers
Name Email Commits
sarthakpati s****i@h****m 194
Sarthak Pati s****i@p****u 11
dependabot[bot] 4****]@u****m 1
Committer Domains (Top 20 + Academic)
pennmedicine.upenn.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 4
  • Total pull requests: 12
  • Average time to close issues: about 5 hours
  • Average time to close pull requests: 2 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 13 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sarthakpati (4)
Pull Request Authors
  • sarthakpati (11)
  • dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 21 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 20
  • Total maintainers: 1
pypi.org: labelfusion

Label fusion strategies for multi-class labels.

  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 21 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 14.2%
Stargazers count: 17.7%
Average: 18.5%
Dependent repos count: 21.8%
Downloads: 28.7%
Maintainers (1)
sarthakpati
Last synced: 6 months ago
conda-forge.org: labelfusion
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 46.9%
Forks count: 49.6%
Dependent packages count: 51.2%
Stargazers count: 52.6%
Last synced: 6 months ago

Dependencies

.github/workflows/publish-on-pypi.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite
setup.py pypi