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clinicadl-zoo

Community transforms and models for ClinicaDL.

https://github.com/aramis-lab/clinicadl-zoo

Science Score: 44.0%

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
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    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Community transforms and models for ClinicaDL.

Basic Info
  • Host: GitHub
  • Owner: aramis-lab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 241 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Created 11 months ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License Citation

README.md

ClinicaDL Zoo

ClinicaDL Zoo hosts a collection of transforms and models compatible with ClinicaDL.

Contributing to ClinicaDL Zoo will make your work fully compatible with ClinicaDL, and thus fully reproducible. It will also benefit the community.

Getting started

Currently, ClinicaDL 2.0 is in beta mode, so make sure you are on the branch clinicadl_v2 and in the right ClinicaDL environment, and run the command:

poetry install --extras zoo `

NOTE: In the future, ClinicaDL Zoo will be downloaded via: pip install clinicadl[zoo]

Then, you can easily access all transforms and models in the zoo, and use them in clinicadl:

```python

from clinicadl_zoo.transforms.config import NanRemovalConfig from clinicadl.transforms.config import ZNormalizationConfig from clinicadl.transforms import Transforms

transforms = Transforms(imagetransforms=[NanRemovalConfig(), ZNormalizationConfig()]) transforms.gettransforms()[0] Compose([NanRemoval(nan=0.0, posinf=None, neginf=None), ZNormalization(masking_method=None)]) ```

Contributing

To add your transforms or models to ClinicaDL Zoo, you need to open a Pull Request on this repository. To do this, please follow to relevant tutorial:

Prerequisite

To contribute, you need:

  1. a Python environment with ClinicaDL installed in developer mode (i.e. via poetry and not via pip);

  2. to clone this repository (ideally, fork it first):

    git clone https://github.com/aramis-lab/clinicadl-zoo.git

  3. to install some developing tools: cd clinicadl-zoo pre-commit install

Owner

  • Name: ARAMIS Lab
  • Login: aramis-lab
  • Kind: organization
  • Location: Paris, France

The Aramis Lab is a joint research team between CNRS, Inria, Inserm and Sorbonne University and belongs to the Paris Brain Institute (ICM).

Citation (CITATION.cff) 

cff-version: 0.1.0
message: If you use this software, please cite it as below.
authors:
  - family-names: de Varax
    given-names: Thibault
  - family-names: Brianceau
    given-name: Camille
title: "ClinicaDL ZOO: Community transforms and models for ClinicaDL"
version: 0.1.0
license: MIT
date-released: 2025-04-08
url: "https://github.com/aramis-lab/clinicadl-zoo"

GitHub Events

Total
  • Watch event: 1
  • Delete event: 1
  • Push event: 26
  • Pull request review comment event: 9
  • Pull request review event: 4
  • Pull request event: 4
  • Fork event: 2
  • Create event: 3
Last Year
  • Watch event: 1
  • Delete event: 1
  • Push event: 26
  • Pull request review comment event: 9
  • Pull request review event: 4
  • Pull request event: 4
  • Fork event: 2
  • Create event: 3

Issues and Pull Requests

Last synced: 7 months ago