Open Science Examples¶
Welcome to the examples section of the handbook! This section is organized by scientific disciplines. We are actively collecting research projects that have implemented open science practices. Please feel free to open a pull request to include your work here. There are no restrictions on what can be added. We are seeking to share a diverse set of open science research projects.
For guidance on opening a pull request, please refer to our contributing guide or ask Franklin (GitHub: @franklin-feingold, Email: ffein@stanford.edu). Please feel free to ask Franklin any other questions you may have!
Psychological science¶
Inhibition-induced devaluation (Patrick Bissett et al.)¶
An example of a complete Python-based workflow for analyzing a cognitive psychology dataset
Open science components: Code Sharing, Data Sharing, Reproducible Analysis
Code and data: Github
Still suspicious: The suspicious coincidence effect revisited (Molly Lewis & Michael C. Frank)¶
An example of a set of pre-registered developmental psychology studies.
Open science components: Pre-registration, Code Sharing, Data Sharing, Reproducible Manuscript
Pre-registration: Open Science Framework
Code and data: Github
Neuroimaging Analysis Replication and Prediction Study (Botvinik-Nezer et al.)¶
An example of a fully reproducible and automated neuroimaging analysis workflow using continuous integration
Open science components: Pre-registration, Code Sharing, Data Sharing, Reproducible Analysis
Pre-registration (prediction market component): Open Science Framework
Data: OpenNeuro, Zenodo (primary data) and Zenodo (analysis outputs)
Ensemble Tractography¶
The Ensemble Tractography share the code and data to reproduce the publication figures.
Open science components: data sharing, code sharing
Code: GitHub
mrQ software¶
The mrQ software package shares the data and code to reproduce the quantitative map outputs.
Open science components: data sharing, code sharing
Code: GitHub
A major human white-matter pathway between dorsal and ventral visual cortex¶
This project shares the code and data to reproduce the manuscript figures.
Open science components: data sharing, code sharing
Data and Code: Stanford Digital Repository
LiFE Demo¶
The LiFE demo shares the code and demo data.
Open science components: data sharing, code sharing
Code: GitHub
Asynchronous broadband signals are the principal source of the BOLD response in human visual cortex¶
This project shares the code and data to reproduce the manuscript figures.
Open science components: data sharing, code sharing
Data and Code: Stanford Digital Repository
Human brain diffusion-weighted MRI, collected with high diffusion-weighting angular resolution and repeated measurements at multiple diffusion-weighting strengths¶
This project shares the code and data.
Open science components: data sharing, code sharing
Code: GitHub
Human brain diffusion-weighted MRI, fiber tractography and validation¶
This project shares the code and data.
Open science components: data sharing, code sharing
Code: GitHub
Quantifying the local tissue volume and composition in individual brains with MRI¶
This project shares the code and data.
Open science components: data sharing, code sharing
Code: GitHub
Magnetic Resonance Spectroscopy data for testing and examples of the Stanford CNI MRS Analysis Library (SMAL)¶
This project shares the data and analysis library.
Open science components: data sharing, code sharing
Analysis library: GitHub
Test-retest Diffusion MRI, measured at 1.5 mm isotropic resolution, b-value=2000 s/mm^2¶
This project shares the data and analysis library.
Open science components: data sharing, code sharing
Analysis library: GitHub
Image Systems Engineering¶
Underwater Image Systems Simulation¶
The Underwater Image Systems Stimulation shares a collection of tools to closely simulate the appearance of underwater scenes in a variety of water conditions.
Open science components: data sharing, code sharing
Code: GitHub
Computational Multispectral Flash¶
The Computational Multispectral Flash shares the data and Matlab implementation to investigate how an adjustable multispectral flash to modify the spectral illumination of a scene.
Open science components: data sharing, code sharing
Code: GitHub
Designing illuminant spectral power distribution for surface classification¶
Designing illuminant spectral power distribution for surface classification shares the data and tools to estimate the optimal spectral power distribution of the illuminant.
Open science components: data sharing, code sharing
Code: GitHub
Learning the Image Processing Pipeline¶
Learning the Image Processing Pipeline shares the data and tools to show how the method has been used to design pipelines for novel sensor architectures in consumer photography applications.
Open science components: data sharing, code sharing
Code: GitHub
Simultaneous surface reflectance and fluorescence¶
Simultaneous surface reflectance and fluorescence shares the data and toolbox to illustrate how to jointly estimate the reflectance and fluorescence from a single set of images acquired under multiple illuminants.
Open science components: data sharing, code sharing
Code: GitHub
Social science¶
Stanford Open Policing Project¶
The Stanford Open Policing Project collects, standardizes, and publicly shares data on vehicle and pedestrian stops from law enforcement departments across the country. They have gathered over 200 million records from dozens of state and local police departments across the country.
Open science components: data sharing, code sharing, reproducible data analysis
Data: Project website
Code and data analysis: GitHub. The reproducible data analysis can be found on their GitHub by looking at their README.