Tools for Managing Imaging FlowCytobot (IFCB) Data
Function to Create MANIFEST.txt
Defunct functions
Adjust Classifications in Manual Annotations
Annotate IFCB Images with Specified Class
Create Manual Classification MAT Files from PNG Subfolders
Convert IFCB Filenames to Timestamps
Correct Annotations in MATLAB Classlist Files
Count IFCB Annotations from .mat Files
Create a class2use .mat File
Create an Empty Manual Classification MAT File
Create a MANIFEST.txt File
Create a Manual Classification MAT File
Download IFCB data files from an IFCB Dashboard
Download metadata from the IFCB Dashboard API
Download Test IFCB Data
Download and Extract WHOI-Plankton Data
Extract Annotated Images from IFCB Data
Extract Biovolumes from IFCB Data and Compute Carbon Content
Extract Taxa Images from MATLAB Classified Sample
Extract Images from IFCB ROI File
Get EcoTaxa Column Names
Retrieve Ferrybox Data for Specified Timestamps
Get Variable Names from a MAT File
Get Classes from a MAT File
Read IFCB Header File and Extract Runtime Information
Get Shark Column Names
Get Shark Column Example
Get Trophic Type for a List of Plankton Taxa
Identify Diatoms in Taxa List
Check if Points are in a Specific Sea Basin
Determine if Positions are Near Land
Download bin list from the IFCB Dashboard API
Retrieve WoRMS Records with Retry Mechanism
Merge IFCB Manual Classification Data
Download and Prepare WHOI-Plankton Data
Generate PSD Plot for a Given Sample
Plot and Save IFCB PSD Data
Install iRfcb Python Environment
Read Feature Files from a Specified Folder or File Paths
Reads HDR Data from IFCB HDR Files
Read a MATLAB .mat File in R
Read and Summarize Classified IFCB Data
Replace Values in MATLAB Classlist
Run IFCB Image Gallery
Summarize Biovolumes and Carbon Content from IFCB Data
Count Cells from TreeBagger Classifier Output
Summarize Image Counts by Class and Sample
Summarize PNG Image Metadata
Estimate Volume Analyzed from IFCB ADC File
Estimate Volume Analyzed from IFCB Header File
Determine if Points are in a Specified Sea Basin
Zip Image Subfolders by Class
Create a Zip Archive of Manual MATLAB Files
Zip PNG Folders
iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data
Process IFCB String
Function to Read Individual Files and Extract Relevant Lines
Retrieve WoRMS Records with Retry Mechanism
Split Large Zip File into Smaller Parts
Summarize TreeBagger Classifier Results
Convert Biovolume to Carbon for Large Diatoms
Convert Biovolume to Carbon for Non-Diatom Protists
A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/en/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.