Diagnostic Image Analysis Group (@DIAGNijmegen)
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DIAGNijmegen

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Top repositories

1

neural-odes-segmentation

Neural Ordinary Differential Equations for Semantic Segmentation of Individual Colon Glands
Python
105
star
2

StreamingCNN

To train deep convolutional neural networks, the input data and the activations need to be kept in memory. Given the limited memory available in current GPUs, this limits the maximum dimensions of the input data. Here we demonstrate a method to train convolutional neural networks while holding only parts of the image in memory.
Jupyter Notebook
97
star
3

pathology-whole-slide-data

A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.
Python
89
star
4

pathology-streaming-pipeline

Use streaming to train whole-slides images with single image-level labels, by reducing GPU memory requirements with 99%.
Python
75
star
5

pathology-he-auto-augment

H&E tailored Randaugment: automatic data augmentation policy selection for H&E-stained histopathology.
Python
52
star
6

pathology-hooknet

Jupyter Notebook
51
star
7

picai_labels

Annotations for the PI-CAI Challenge: Public Training and Development Dataset
47
star
8

picai_baseline

Baseline AI models for 3D csPCa detection/diagnosis in bpMRI
Python
42
star
9

prostateMR_3D-CAD-csPCa

Hierarchical probabilistic 3D U-Net, with attention mechanisms (β€”π˜ˆπ˜΅π˜΅π˜¦π˜―π˜΅π˜ͺ𝘰𝘯 𝘜-π˜•π˜¦π˜΅, π˜šπ˜Œπ˜™π˜¦π˜΄π˜•π˜¦π˜΅) and a nested decoder structure with deep supervision (β€”π˜œπ˜•π˜¦π˜΅++). Built in TensorFlow 2.5. Configured for voxel-level clinically significant prostate cancer detection in multi-channel 3D bpMRI scans.
Python
39
star
10

HoVer-UNet

Python
28
star
11

pathology-artifact-detection

Quality control of whole-slide images through multi-class semantic segmentation of artifacts
Python
27
star
12

ULS23

Repository for the Universal Lesion Segmentation Challenge '23
Python
26
star
13

picai_prep

Preprocessing 3D medical images and image archives β€”geared towards prostate cancer detection in MRI.
Python
18
star
14

picai_eval

Evaluation of 3D detection and diagnosis performance β€”geared towards prostate cancer detection in MRI.
Python
18
star
15

Report-Guided-Annotation

Report Guided Annotation
Python
18
star
16

spgnn

Structure and position aware graph neural network for airway labeling
Python
13
star
17

opencxr

A collection of open-source algorithms for chest X-ray analysis
Python
13
star
18

rse-panimg

Conversion of medical images to MHA and TIFF.
Python
13
star
19

AbdomenMRUS-prostate-segmentation

Grand Challenge wrapper for whole-gland prostate segmentation with nnUNet
Python
13
star
20

SPIDER-Baseline-IIS

Python
13
star
21

panda-challenge

Code related to the PANDA challenge on artificial intelligence for Gleason grading
Jupyter Notebook
12
star
22

pathology-hooknet-tls

Jupyter Notebook
9
star
23

pathology-tiger-algorithm-example

Example algorithm and docker for the TIGER challenge
Python
8
star
24

pathology-tiger-baseline

Python
6
star
25

panorama_labels

6
star
26

drive-vessels-unet

Python
6
star
27

pathology-whole-slide-packer

extracts tissue sections from one or multiple whole slide images and combines them into a single new slide removing excess white space
Python
5
star
28

website-content

This repository stores all the content for the diag websites.
TeX
5
star
29

covid19-imaging-ai

An organized collection of data, software, initiatives and papers for COVID-19 imaging AI
4
star
30

pathology-he-autoaugmetation

Comparative analysis of 4 state-of-the-art automatic augmentation algorithms in H&E stained histopathology.
Python
4
star
31

MedicalTransferLearning3D-UNet

This repository contains the model used for the paper ''Transfer learning from a sparsely annotated dataset of 3D medical images'' by G. Humpire, C. Jacobs, M. Prokop, B. van Ginneken, N. Lessmann.
Jupyter Notebook
4
star
32

prostateMR-USSL

Uncertainty Aware Self-Supervised Prostate Zonal Segmentation in 3D MRI scans using Probabilistic Attention U-Net..
Python
3
star
33

picai_nnunet_gc_algorithm

nnUNet model for 3D csPCa detection/diagnosis in bpMRI, deployable on grand-challenge.org
Python
3
star
34

picai_nndetection_semi_supervised_gc_algorithm

Semi-supervised nnDetection model for 3D csPCa detection/diagnosis in bpMRI, deployable on grand-challenge.org
Python
3
star
35

AbdomenMRUS-csPCa-CAD-nnUNet

Clinically Significant Prostate Cancer Detection in bpMRI using models trained with Report Guided Annotations
Python
3
star
36

pathology-streamingclam

Lightstream implementation of the StreamingCLAM model
Python
3
star
37

PANORAMA_baseline

Python
3
star
38

picai_unet_semi_supervised_gc_algorithm

Semi-supervised UNet model for 3D csPCa detection/diagnosis in bpMRI, deployable on grand-challenge.org
Python
3
star
39

bodyct-dsb2017-grt123

Repository which contains the code of the grt123 solution from the Kaggle DSB 2017 challenge on lung cancer detection
Python
2
star
40

picai_unet_gc_algorithm

U-Net model for 3D csPCa detection/diagnosis in bpMRI, deployable on grand-challenge.org
Python
2
star
41

picai_nnunet_semi_supervised_gc_algorithm

Semi-supervised nnUNet model for 3D csPCa detection/diagnosis in bpMRI, deployable on grand-challenge.org
Python
2
star
42

adhesion_detection

Adhesion detection on cine MRI
Jupyter Notebook
2
star
43

rse-gcapi

Python client for the grand-challenge.org API
Python
2
star
44

flare22-brananas

Codebase of team brananas for the FLARE22 challenge
Python
2
star
45

picai_nndetection_gc_algorithm

nnDetection model for 3D csPCa detection/diagnosis in bpMRI, deployable on grand-challenge.org
Python
2
star
46

ACOUSLIC-AI-baseline

Python
2
star
47

ACOUSLIC-AI-evaluation-method

Python
2
star
48

SPIDER-Evaluation

Evaluation code used for the SPIDER Challenge.
Python
2
star
49

bodyct-luna22-ismi-training-baseline

Baseline repo for LUNA22-ismi challenge
Python
2
star
50

stoic2021-finalphase-submission-hal9000

Python
1
star
51

stoic2021-finalphase-submission-code1055

Jupyter Notebook
1
star
52

bodyct-dram

Python
1
star
53

node21-noduledetection

Template for nodule detection algorithm for node21 challenge
Jupyter Notebook
1
star
54

frodo

library for FRODO
Python
1
star
55

node21

1
star
56

m-heads

Python
1
star
57

rse-pyswot

Python implementation of JetBrains/swot
Python
1
star
58

LEOPARD-challenge-baseline

Python
1
star
59

rse-sagemaker-shim

Adapts algorithms that implement the Grand Challenge inference API for running in SageMaker
Python
1
star
60

CE-CT_PDAC_AutomaticDetection_nnUnet

Fully automtic pipeline for pancreatic ductal adenocarcinoma (PDAC) detection on contrast enhanced computed tomography (CE-CT) scans
Python
1
star
61

auc23-t2-algorithm-container-rib-ct-fracture

Python
1
star