I 'R' FlowCytobot (iRfcb): Tools for Managing Imaging FlowCytobot (IFCB) Data

Overview

The iRfcb R package offers a suite of tools for managing and performing quality control on plankton data generated by the Imaging FlowCytobot (IFCB). It streamlines the processing and analysis of IFCB data, facilitating the preparation of IFCB data and images for publication (e.g. in GBIF, OBIS, EMODNet, SHARK or EcoTaxa). It is especially useful for researchers using, or partly using, the MATLAB ifcb-analysis package.

Key Features

• Data Management: Functions for reading raw and processed IFCB files, counting and summarizing annotated and classified image data, correcting and merging manually annotated datasets.
• Quality Control: Tools for geospatial quality control of IFCB data and analysis of Particle Size Distribution.
• Image Extraction: Tools to extract and prepare images for publication.
• Taxonomical Data: Tools for handling and analyzing taxonomic data and calculating biomass concentration from image data.

Installation

You can install iRfcb from CRAN using:

install.packages("iRfcb")

Development version

To access a feature from the development version of iRfcb, install the latest development version from GitHub using the remotes package:

# install.packages("remotes")
remotes::install_github("EuropeanIFCBGroup/iRfcb")

Some functions in iRfcb require Python. You can download Python from the official website: python.org/downloads. For more details, please visit the project's webpage.

Documentation and Tutorials

Reference

For a detailed overview of all available iRfcb functions, please visit the reference section:

• Function Reference

Tutorials

Explore the key features and capabilities of iRfcb through the tutorials:

• iRfcb Introduction
• Quality Control of IFCB Data
• Handling MATLAB Results
• Creating a DwC-A from IFCB Data
• Sharing Annotated IFCB Images
• Prepare IFCB Images for EcoTaxa

Example Usage

iRfcb is designed for integration into IFCB data processing pipelines. For an example, see its implementation in the following project:

• Example Data Pipelines

Getting help

If you encounter a bug or need an IFCB feature that’s missing, please report it on GitHub with a minimal reproducible example.

Repository

For more details and the latest updates, visit the GitHub repository.

License

This package is licensed under the MIT License.