All software

mri_distortion_toolkit

A toolkit to correct geometric distortion in MR images. Includes tools for converting DICOM to NIfTI, and generating distortion correction maps.

MSS-IMProv

An Integrative Modeling Platform

mudicom

A Python library for interacting with DICOM files. Provides a simpler, more intuitive interface than other libraries.

MUSIMAN

In summary, the MUSIMAN package is a software tool to ease the parallelization of simulations run with the Monte Carlo code PENELOPE 2014

NanopubJL

JupyterLab extension to aid in searching and publishing of Nanopublications in a python notebook

Nature Counts

The NatureCounts platform allows users to collect, archive, interpret and access wildlife data to advance the understanding of bird populations across the Western Hemisphere.

NDVItoTaskmap

A browser-based open-source tool for calculating 20+ vegetation indices from drone GeoTIFF imagery and generating variable-rate prescription task maps (ISOXML, Shapefile, GeoJSON) integrated with Dutch BRP parcel data.

nedextract

nedextract is a python library that helps you to extract information on person names and organisations mentioned in Dutch (annual report) PDF files.

NetCDF2LittleR

An application to convert NetCDF files to the Little-R format

Network Simulation Engine

A modular financial risk management and policy-laboratory tool: simulates financial network topologies and translates them into liquidity outcomes, enabling evaluation of early-warning triggered dynamic buffers and central bank backstops for mitigating systemic liquidity shortfalls.

NeuroAnalyzer

NeuroAnalyzer is a Julia toolbox for analyzing neurophysiological data.

NeuroGym

NeuroGym is a curated collection of neuroscience tasks with a common interface. The goal is to facilitate the training of neural network models on neuroscience tasks.

NIM-Studio

nnU-Net

nnU-Net is a semantic segmentation method that automatically adapts to a given dataset. It will analyze the provided training cases and automatically configure a matching U-Net-based segmentation pipeline.

Noodle Biomedical Literature Discovery

Public, read-only biomedical literature search, publication inspection, and bounded citation and semantic graph traversal through a hosted MCP server.

NPLinker eScience Workshop GenMetMine Materials

These materials were used as a part of the NPLinker eScience Workshop on Natural Product Genome & Metabolome Mining: https://www.wur.nl/en/research-results/chair-groups/plant-sciences/bioinformatics/teaching/nplinker_workshop.htm Most materials are available in a format facilitating its reuse.

Nunaliit

The Nunaliit Atlas Framework aims to make it easy to tell stories and highlight relationships between many different forms of information from a variety of sources, using maps as a central way to connect and interact with the data.

OBiBa Agate

Agate is a web application that offers users related services to the OBiBa software stack.

OBiBa Mica

Mica is OBiBa's software application that is used to create data web portals for large-scale epidemiological studies or multiple-study consortia.

OBiBa Opal

Opal is OBiBa's core data repository application for epidemiological studies.

Ocean Networks Canada

By bringing data to the surface, ONC provides ocean intelligence to scientists, governments, organizations, and citizens. Ocean data are archived, processed and made freely available via ONC’s data management system, Oceans 3.0.

OCTSEG

Analyze retinal optical coherence tomography images.

OMG Dosimetry

A Python package for performing dosimetry calculations and quality assurance tests. Provides a simple API for common dosimetry tasks.

One button compute

Web application for running a CWL workflow on a bunch of files.

OnkoDICOM

Cross-platform. Provides DVH output, clinical data capture (radiomics), Pyradiomics output, anonymization, ROI manipulation.

OpenDA

Open data assimilation toolbox. OpenDA is an open interface standard for a set of tools to quickly implement data-assimilation and calibration for arbitrary numerical models.

Open Matrices Stimulus Set (omss)

omss is a Python package for generating matrix reasoning puzzles, inspired by Raven's Progressive Matrices. It allows users to generate an unlimited number of customizable puzzles across a range of difficulty levels by setting rules for visual elements.

OpenRefine

OpenRefine is a powerful free, open source tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.

OpenREGGUI

Image processing, open-source platform for research in proton therapy

OpenSim Creator

A UI for building OpenSim models

OpenTPS

OpenTPS is an open-source treatment planning system (TPS) for research in radiation therapy and proton therapy.

opynsim

Python-Native Musculoskeletal Modelling

Orange3 Argument Mining Add-on

This open-source Python package facilitates the processing, analysis, and visualization of argument corpora. Additionally, It offers user-friendly GUIs integrated into the Orange3 scientific workflow platform, enabling non-programmers to utilize its capabilities.

Orange3 Story Navigator

Add-on providing quantitative textual story analysis based on principles in narrative psychology

Orange Hackathon

Orange modules for text processing in the project What Works When for Whom

Orthanc

Orthanc is a Belgian, open-source, lightweight DICOM server for healthcare and medical research.

OsiriX

Widely used DICOM viewer. Supports 2D, 3D, 4D, 5D viewing.

Osmium

Start, stop and monitor applications remotely via a HTTP interface.

oTree Demo Experiments

oTree demo experiment: Public goods game

oTree Development Environment

A Docker environment for programming against multiple oTree server

oTree Waiting Room

A load balancer for oTree servers.

Overture Arranger

Data can be messy, let Arranger organize it for you.

Overture Data Management System

Overture is a collection of open-source, extendable solutions for big-data genomic science that research institutions and individual researchers can use to support their work.

Overture Ego

A stateless authorization and user management service.

Overture Maestro

Organizing your distributed data into one index.

Overture Score

Transfer data quickly and easily to and from any cloud-based storage system.

Overture Song

Quickly and reliably track genome metadata scattered across multiple Cloud storage systems.

PACTE

A Collaborative Electronic Text Annotation Platform