biopixR: Extracting Insights from Biological Images
Creators: name: Brauckhoff, Tim
name: Rödiger, Stefan
Publisher: name: Zenodo
Year: 2024
Subjects: subject: Medical biotechnology
subject: FOS: Medical biotechnology

description: biopixR - Extended Vignette for Bioimage Analysis Package in R

This is the extended vignette for our R package biopixR (v 1.1.0) dedicated to the analysis of bioimage data, with a specialized focus on spherical objects such as microplastics, microbeads and cellular foci (DNA damage). This comprehensive guide is designed to enhance your understanding and utilization of the package, providing detailed information about its functions and practical applications for your research.

Key Features of the Vignette



Introduction to biopixR   - Overview of bioimage analysis and its importance in biological research.   - History, Philosophy and Aim of the package.

Package Installation and Setup   - Step-by-step instructions for installing the package from CRAN or GitHub.

Detailed Function Descriptions   - In-depth explanations of each function included in the package.   - Example code snippets to demonstrate function usage.   - Visual examples to illustrate the output of each function.

Data Preprocessing   - Techniques for image filtering, and enhancement.   - Methods to segment spherical objects from complex backgrounds.

Object Detection and Quantification   - Algorithms for detecting spherical objects within bioimages.   - Parameters for tuning the detection process for accuracy and efficiency.   - Functions to measure and analyze properties of detected objects (e.g., size, count, intensity).

Advanced Analysis Techniques   - Procedures for tracking movement and changes in spherical objects over time.   - Statistical methods for analyzing object distribution and spatial relationships.   - Integrating bioimage analysis results with other data types for comprehensive studies.

Case Studies and Applications   - Real-world examples demonstrating the application of the package to various research problems.   - Case studies on analyzing microbeads and DNA damage.   - Discussion of challenges encountered and solutions applied.


Conclusion

This extended vignette aims to equip researchers with the tools and knowledge necessary to effectively analyze bioimage data, with a particular emphasis on spherical objects. By leveraging the functions and techniques described in this guide, you can enhance the accuracy and depth of your bioimage analyses, leading to more robust and insightful research outcomes.

We invite you to explore the extended vignette and utilize its resources to advance your work in bioimage analysis. Your feedback and contributions are invaluable as we continue to improve and expand the package.

Package Repository: https://github.com/Brauckhoff/biopixR // DOI: https://doi.org/10.32614/CRAN.package.biopixR

For any questions or further assistance, please contact us via GitHub.

We look forward to seeing the innovative ways you apply our package to your research.

The biopixR Package Development Team

 

Funding

The study was funded in part by the project Rubin: NeuroMiR (03RU1U051A, federal ministry of education and research, Germany).