All software

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.

calibr8

calibr8 is a Python toolbox for likelihood-based calibration modeling and Bayesian inference. It supports uni- and multivariate problems, continuous & discrete distributions and includes ready to use models for many non-linear problems. It integrates with PyMC for advanced Bayesian inference.

CellDetection

An open-source Python package, offering advanced AI methods for the identification and segmentation of biomedical objects, such as cells, in image data. Includes trained models that work out-of-the-box for a wide range of use cases.

CellRank

CellRank is a computational framework to study cellular fate decisions based on various types of single-cell genomics data. CellRank scales to large cell numbers, is fully compatible with the scverse ecosystem, and is easy to use.

Earth System Model Evaluation Tool (ESMValTool)

Emipy

Emipy is a Python package to access, manipulate, analyze and visualize data on various pollutants, which is collected in the European Pollutant Release Register (E-PRTR). Therefore, it enables the easy use of this data for research in different fields (e.g., public health or energy system analysis).

ESMValCore

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.

FatSegNet

A fully automated deep learning pipeline for adipose tissue (visceral and subcutaneous) segmentation on abdominal Dixon MRI.

FSQC

This package provides quality assurance / quality control scripts for FastSurfer- or FreeSurfer-processed structural MRI data.

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.

Heat

Heat is a flexible and seamless open-source software for high performance data analytics and machine learning. It provides highly optimized algorithms and data structures for tensor computations using CPUs, GPUs and distributed cluster systems on top of MPI.