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Related Experiment Video

Updated: Jan 10, 2026

Using Computer Vision Libraries to Streamline Nuclei Quantification

Using Computer Vision Libraries to Streamline Nuclei Quantification

Published on: June 6, 2025

QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research.

Jure Demšar^1,2, Aleksij Kraljič², Andraž Matkovič^2,3,4

¹Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.

Biorxiv : the Preprint Server for Biology

|November 26, 2025

Summary

This summary is machine-generated.

QuNex recipes simplify complex neuroimaging data analysis by providing a transparent framework for reproducible workflows. This ensures detailed documentation and easy replication of neuroimaging studies.

Keywords:

data analysis data processing neuroimaging reproducibility

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Area of Science:

Neuroimaging
Computational Neuroscience
Data Science

Background:

Neuroimaging data preprocessing and analysis are complex, requiring multiple tools and parameter tuning.
Current methods often lack sufficient detail for complete transparency and reproducibility.
This complexity hinders the sharing and replication of neuroimaging workflows.

Purpose of the Study:

To introduce QuNex recipes, a framework for defining and executing complete neuroimaging workflows.
To enhance transparency, reproducibility, and standardization in neuroimaging data processing.
To facilitate the seamless integration of various tools and custom scripts within a unified platform.

Main Methods:

Developed QuNex recipes as an integrated feature of the Quantitative Neuroimaging Environment & Toolbox (QuNex).
Recipes define and execute end-to-end neuroimaging workflows in a machine- and human-readable format.
The framework captures all processing steps and parameter settings for complete documentation.

Main Results:

QuNex recipes enable transparent, machine- and human-readable definition of neuroimaging workflows.
The framework allows seamless integration of QuNex commands, custom scripts, and external tools.
Sharing the QuNex version, recipe file, and data allows for one-command replication of studies.

Conclusions:

QuNex recipes standardize workflow specification and enhance transparency in neuroimaging research.
This framework facilitates the reproducible sharing of complex neuroimaging analyses.
Recipes promote the open exchange of best practices and reproducible methods within the neuroimaging community.