24 projects
AVID
AVID is a Python framework for declarative, data-driven processing of large-scale image datasets, particularly designed for biomedical image analysis workflows.
ParticleSeg3D
Scalable, out-of-the box segmentation of individual particles from mineral samples acquired with micro CT
tqdmp
Multiprocessing with tqdm progressbars!
radtract
Radiomic Tractometry for advanced along-tract analysis of diffusion-weighted MRI
voxtell
Free-Text Promptable Universal 3D Medical Image Segmentation
hd-gliomouse
Tool for brain tumor segmentation in mice. This is the result of a joint project between the Department of Neuroradiology at the Heidelberg University Hospital and the Division of Medical Image Computing at the German Cancer Research Center (DKFZ). See readme.md for more information
patchly
A grid sampler for N-dimensional images
napari-mzarr
A reader and writer plugin for the Mzarr image format.
hd-glio
Tool for brain tumor segmentation. This is the result of a joint project between the Department of Neuroradiology at the Heidelberg University Hospital and the Division of Medical Image Computing at the German Cancer Research Center (DKFZ). See readme.md for more information
acvl-utils
Super cool utilities that we just love to use
mzarr
Mzarr (Multi-Resolution Zarr) is a Python library for working with the Mzarr image format
cmdint
Enables detailed logging of command line calls in a very lightweight manner.
nnunetv2
nnU-Net is a framework for out-of-the box image segmentation.
nnunet
nnU-Net. Framework for out-of-the box biomedical image segmentation.
mitk-python
Python bindings for the Medical Imaging Interaction Toolkit (MITK)
napari-nifti
napari reader and writer for medical images (NIfTI, NRRD, MetaImage, MGH/MGZ, DICOM) through MedVol, with correct physical geometry and orientation.
batchgenerators
Data augmentation toolkit
napari-sam
Segment anything with Meta AI's new SAM model!
dynamic-network-architectures
none
HD-BET
Tool for brain extraction
batchgeneratorsv2
Batchgenerators but better
napari-nninteractive
nnInteractive plugin for Napari
nnInteractive
Inference code for nnInteractive
nninteractive-client
Lightweight, torch-free remote client for nnInteractive (nnInteractiveRemoteInferenceSession)
