German Center for Neurodegenerative Diseases
BrainPrint
Our BrainPrint tools provide shape descriptors of neuroanatomical structures and require a FreeSurfer or FastSurfer segmentation as a pre-processing step. BrainPrint is based on “ShapeDNA” a spectral shape descriptor.
- Data analysis
- MRI
- open source
- + 1
- Python
cyCONDOR
cyCONDOR, an easy-to-use computational framework for end-to-end High-Dimensional Cytometry data analysis. cyCONDOR offers guided pre-processing, clustering, dimensionality reduction, machine learning, pseudotime analysis, and batch integration, making it ideal for clinical and research settings.
- Data Visualization
- Health
- Machine learning
- + 2
- R
FastSurfer
FastSurfer is a fast and accurate deep-learning pipeline for the analysis of human brain MRI. FastSurfer provides a fully compatible FreeSurfer alternative for volumetric and surface-based thickness analysis, also supporting sub-mm resolutions, and sub-segmentation of neuroanatomical structures.
- Data analysis
- Deep Learning
- Image processing
- + 3
- Jupyter Notebook
- Python
- Shell
- + 1
FatSegNet
A fully automated deep learning pipeline for adipose tissue (visceral and subcutaneous) segmentation on abdominal Dixon MRI.
- Data analysis
- MRI
- open source
- Python
- Dockerfile
- Shell
FSQC
This package provides quality assurance / quality control scripts for FastSurfer- or FreeSurfer-processed structural MRI data.
- Data analysis
- MRI
- Neuroimaging
- + 2
- Python
- Dockerfile
hCoCena - horizontal integration and analysis of transcriptomics datasets
hCoCena is an R-package that allows you to comprehensively and easily analyse your transcriptomics data. It also provides the option to integrate several datasets using a network-based integration approach and analyse them jointly. Tutorials and a Docker image exist to help you get to know the tool.
- Data analysis
- Gene Expression
- Health
- + 1
- R
HIPSTA
The HIPpocampal Shape and Thickness Analysis Toolbox (HIPSTA) present a geometry-based method for the analysis of local hippocampal thickness and curvature and constructs an intrinsic coordinate system (unrolling/flattening) for statistical analysis across multiple participants.
- MRI
- Neuroimaging
- open source
- + 1
- Python
- Dockerfile
InteractiveVis
The InteractiveVis software framework provides a blueprint for evaluating 3D datasets with convolutional neural networks (CNNs), and for deriving and visualizing CNN relevance maps. This tool was developed and tested for disease detection in MRI scans. We plan to extend it to other domains.
- Data Visualization
- MRI
- open source
- + 1
- Jupyter Notebook
- HTML
- MATLAB
- + 5
JEMRIS
JEMRIS is a versatile, open-source, multi-purpose MRI simulator. It is well-suited for research and education.
- MRI
- Simulation
- C++
- Python
- MATLAB
- + 5
LaPy
LaPy is an open-source Python package for differential geometry on triangle and tetrahedra meshes. It includes an FEM solver to estimate the Laplace, Poisson or Heat equations, also the computations of gradients, divergence, mean-curvature flow, conformal mappings, geodesics, ShapeDNA and more.
- computational geometry
- FEM
- Laplace
- + 4
- Python