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MIC-DKFZ

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Top repositories

1

nnUNet

Python
4,806
star
2

medicaldetectiontoolkit

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
Python
1,258
star
3

batchgenerators

A framework for data augmentation for 2D and 3D image classification and segmentation
Jupyter Notebook
1,036
star
4

nnDetection

nnDetection is a self-configuring framework for 3D (volumetric) medical object detection which can be applied to new data sets without manual intervention. It includes guides for 12 data sets that were used to develop and evaluate the performance of the proposed method.
Python
508
star
5

HD-BET

MRI brain extraction tool
Python
230
star
6

trixi

Manage your machine learning experiments with trixi - modular, reproducible, high fashion. An experiment infrastructure optimized for PyTorch, but flexible enough to work for your framework and your tastes.
Python
220
star
7

TractSeg

Automatic White Matter Bundle Segmentation
Python
212
star
8

napari-sam

Python
206
star
9

MedNeXt

MedNeXt is a fully ConvNeXt architecture for 3D medical image segmentation (MICCAI 2023).
Python
205
star
10

basic_unet_example

An example project of how to use a U-Net for segmentation on medical images with PyTorch.
Python
132
star
11

BraTS2017

Python
74
star
12

LIDC-IDRI-processing

Scripts for the preprocessing of LIDC-IDRI data
Python
71
star
13

MITK-Diffusion

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit
C++
66
star
14

mood

Repository for the Medical Out-of-Distribution Analysis Challenge.
Python
59
star
15

BodyPartRegression

Python
58
star
16

ACDC2017

Python
53
star
17

niicat

This is a tool to quickly preview nifti images on the terminal
Python
48
star
18

RegRCNN

This repository holds the code framework used in the paper Reg R-CNN: Lesion Detection and Grading under Noisy Labels. It is a fork of MIC-DKFZ/medicaldetectiontoolkit with regression capabilites.
Python
48
star
19

dynamic-network-architectures

Python
42
star
20

MultiTalent

Implemention of the Paper "MultiTalent: A Multi-Dataset Approach to Medical Image Segmentation"
Python
36
star
21

image_classification

🎯 Deep Learning Framework for Image Classification & Regression in Pytorch for Fast Experiments
Python
33
star
22

vae-anomaly-experiments

Python
26
star
23

Hyppopy

Hyppopy is a python toolbox for blackbox optimization. It's purpose is to offer a unified and easy to use interface to a collection of solver libraries.
Python
25
star
24

RTTB

Swiss army knife for radiotherapy analysis
C++
22
star
25

patchly

A grid sampler for larger-than-memory N-dimensional images
Python
20
star
26

probabilistic_unet

A U-Net combined with a variational auto-encoder that is able to learn conditional distributions over semantic segmentations.
Jupyter Notebook
20
star
27

image-time-series

Code for deep learning-based glioma/tumor growth models
Python
20
star
28

semantic_segmentation

Python
20
star
29

anatomy_informed_DA

Python
16
star
30

ParticleSeg3D

Python
9
star
31

gpconvcnp

Code for "GP-ConvCNP: Better Generalization for Convolutional Conditional Neural Processes on Time Series Data"
Python
8
star
32

radtract

RadTract: enhanced tractometry with radiomics-based imaging biomarkers for improved predictive modelling.
Python
8
star
33

cmdint

CmdInterface enables detailed logging of command line and python experiments in a very lightweight manner (coding wise). It wraps your command line or python function calls in a few lines of python code and logs everything you might need to reproduce the experiment later on or to simply check what you did a couple of years ago.
Python
8
star
34

generalized_yolov5

An extension of YOLOv5 to non-natural images together with 5-Fold Cross-Validation
Python
7
star
35

cOOpD

Python
7
star
36

PROUNET

Prostate U-net
Python
7
star
37

MurineAirwaySegmentation

Python
6
star
38

acvl_utils

Python
5
star
39

napari-nifti

Python
4
star
40

OverthINKingSegmenter

Python
3
star
41

agent-sam

Segment Anything model wrapper used by the Medical Imaging Interaction Toolkit (MITK).
Python
3
star
42

help_a_hematologist_out_challenge

Python
2
star
43

napari-mzarr

Python
2
star
44

perovskite-xai

Python
2
star
45

n2c2-challenge-2019

Jupyter Notebook
2
star
46

mzarr

Python
1
star
47

imlh-icml-detection-tools

Python
1
star
48

MatchPoint

MatchPoint is a translational image registration framework written in C++. It offers a standardized interface to utilize several registration algorithm resources (like ITK, plastimatch, elastix) easily in a host application.
C++
1
star