Package: iRfcb 0.9.0.9000

Anders Torstensson

iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

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.

Authors:Anders Torstensson [aut, cre], Kendra Hayashi [ctb], Jamie Enslein [ctb], Raphael Kudela [ctb], Alle Lie [ctb], Jayme Smith [ctb], DTO-BioFlow [fnd], SBDI [fnd]

iRfcb_0.9.0.9000.tar.gz
iRfcb_0.9.0.9000.zip(r-4.7)iRfcb_0.9.0.9000.zip(r-4.6)iRfcb_0.9.0.9000.zip(r-4.5)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iRfcb/json (API)

# Install 'iRfcb' in R:

install.packages('iRfcb', repos = c('https://europeanifcbgroup.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/europeanifcbgroup/irfcb/issues

Pkgdown/docs site:https://europeanifcbgroup.github.io

On CRAN:

data-export imaging-flow-cytometry imaging-flowcytobot oceanography plankton quality-control

5.75 score 3 stars 29 scripts 406 downloads 68 exports 90 dependencies

Last updated from:b48fd7db60. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	235
source / vignettes	OK	262
linux-release-x86_64	OK	236
macos-release-arm64	OK	209
macos-oldrel-arm64	OK	132
windows-devel	OK	185
windows-release	OK	184
windows-oldrel	OK	189
wasm-release	OK	188

Exports:create_package_manifest ifcb_adjust_classes ifcb_annotate_batch ifcb_annotate_samples ifcb_classify_images ifcb_classify_models ifcb_classify_sample ifcb_convert_filenames ifcb_correct_annotation ifcb_count_mat_annotations ifcb_create_class2use ifcb_create_empty_manual_file ifcb_create_manifest ifcb_create_manual_file ifcb_download_dashboard_data ifcb_download_dashboard_metadata ifcb_download_test_data ifcb_download_whoi_plankton ifcb_extract_annotated_images ifcb_extract_biovolumes ifcb_extract_classified_images ifcb_extract_features ifcb_extract_pngs ifcb_get_ecotaxa_example ifcb_get_ferrybox_data ifcb_get_mat_names ifcb_get_mat_variable ifcb_get_runtime ifcb_get_shark_colnames ifcb_get_shark_example ifcb_get_trophic_type ifcb_is_diatom ifcb_is_in_basin ifcb_is_near_land ifcb_list_dashboard_bins ifcb_match_taxa_names ifcb_merge_manual ifcb_prepare_whoi_plankton ifcb_psd ifcb_psd_plot ifcb_py_install ifcb_qc_sample ifcb_read_features ifcb_read_hdr_data ifcb_read_mat ifcb_read_summary ifcb_replace_mat_values ifcb_run_image_gallery ifcb_save_classification ifcb_summarize_biovolumes ifcb_summarize_cell_counts ifcb_summarize_class_counts ifcb_summarize_png_counts ifcb_summarize_png_metadata ifcb_volume_analyzed ifcb_volume_analyzed_from_adc ifcb_which_basin ifcb_zip_images_by_class ifcb_zip_matlab ifcb_zip_pngs process_ifcb_string read_hdr_file retrieve_worms_records split_large_zip summarize_TBclass vol2C_diatom vol2C_lgdiatom vol2C_nondiatom

Dependencies:base64enc bit bit64 bslib cachem class classInt cli clipr commonmark cpp11 crayon crul curl data.table DBI digest dplyr e1071 farver fastmap fontawesome fs generics ggplot2 glue gtable here hms htmltools httpcode httpuv isoband jquerylib jsonlite KernSmooth labeling later lattice lifecycle lubridate magrittr MASS Matrix memoise mime otel pillar pkgconfig png prettyunits progress promises proxy purrr R6 rappdirs RColorBrewer Rcpp RcppTOML readr reticulate rlang rprojroot s2 S7 sass scales sf shiny sourcetools stringi stringr tibble tidyr tidyselect timechange triebeard tzdb units urltools utf8 vctrs viridisLite vroom withr wk worrms xtable zip

iRfcb Introduction

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-07-01
Started: 2025-12-29

Help page	Topics
Function to Create MANIFEST.txt	create_package_manifest
Adjust Classifications in Manual Annotations	ifcb_adjust_classes
Annotate IFCB Images with Specified Class	ifcb_annotate_batch
Create Manual Classification MAT Files from PNG Subfolders	ifcb_annotate_samples
Classify Pre-Extracted IFCB PNG Images Using a Gradio Application	ifcb_classify_images
List Available CNN Models from a Gradio Classification Server	ifcb_classify_models
Classify All Images in an IFCB Sample Using a Gradio Application	ifcb_classify_sample
Convert IFCB Filenames to Timestamps	ifcb_convert_filenames
Correct Annotations in MATLAB Classlist Files	ifcb_correct_annotation
Count IFCB Annotations from .mat Files	ifcb_count_mat_annotations
Create a class2use '.mat' File	ifcb_create_class2use
Create a MANIFEST.txt File	ifcb_create_manifest
Create a Manual Classification MAT File	ifcb_create_manual_file
Download IFCB data files from an IFCB Dashboard	ifcb_download_dashboard_data
Download metadata from the IFCB Dashboard API	ifcb_download_dashboard_metadata
Download Test IFCB Data	ifcb_download_test_data
Download and Extract WHOI-Plankton Data	ifcb_download_whoi_plankton
Extract Annotated Images from IFCB Data	ifcb_extract_annotated_images
Extract Biovolumes from IFCB Data and Compute Carbon Content	ifcb_extract_biovolumes
Extract Taxa Images from Classified Sample	ifcb_extract_classified_images
Extract Slim Features and Blobs from IFCB Data	ifcb_extract_features
Extract Images from IFCB ROI File	ifcb_extract_pngs
Get EcoTaxa Column Names	ifcb_get_ecotaxa_example
Retrieve Ferrybox Data for Specified Timestamps	ifcb_get_ferrybox_data
Get Variable Names from a MAT File	ifcb_get_mat_names
Get Classes from a MAT File	ifcb_get_mat_variable
Read IFCB Header File and Extract Runtime Information	ifcb_get_runtime
Get Shark Column Names	ifcb_get_shark_colnames
Get Shark Column Example	ifcb_get_shark_example
Get Trophic Type for a List of Plankton Taxa	ifcb_get_trophic_type
Identify Diatoms in Taxa List	ifcb_is_diatom
Check if Points are in a Specific Sea Basin	ifcb_is_in_basin
Determine if Positions are Near Land	ifcb_is_near_land
Download bin list from the IFCB Dashboard API	ifcb_list_dashboard_bins
Retrieve WoRMS Records with Retry Mechanism	ifcb_match_taxa_names
Merge IFCB Manual Classification Data	ifcb_merge_manual
Download and Prepare WHOI-Plankton Data	ifcb_prepare_whoi_plankton
Plot and Save IFCB PSD Data	ifcb_psd
Generate PSD Plot for a Given Sample	ifcb_psd_plot
Install iRfcb Python Environment	ifcb_py_install
Quality-control a raw IFCB sample (hdr/adc/roi triplet)	ifcb_qc_sample
Read Feature Files from a Specified Folder or File Paths	ifcb_read_features
Read Data from IFCB HDR Files	ifcb_read_hdr_data
Read a MATLAB .mat File in R	ifcb_read_mat
Read and Summarize Classified IFCB Data	ifcb_read_summary
Replace Values in MATLAB Classlist	ifcb_replace_mat_values
Run IFCB Image Gallery	ifcb_run_image_gallery
Classify an IFCB Sample and Save Results	ifcb_save_classification
Summarize Biovolumes and Carbon Content from IFCB Data	ifcb_summarize_biovolumes
Summarize Diatom Cell Counts and Chain-Length Statistics from IFCB Data	ifcb_summarize_cell_counts
Count Cells from TreeBagger Classifier Output	ifcb_summarize_class_counts
Summarize Image Counts by Class and Sample	ifcb_summarize_png_counts
Summarize PNG Image Metadata	ifcb_summarize_png_metadata
Estimate Volume Analyzed from IFCB Header File	ifcb_volume_analyzed
Estimate Volume Analyzed from IFCB ADC File	ifcb_volume_analyzed_from_adc
Determine if Points are in a Specified Sea Basin	ifcb_which_basin
Zip Image Subfolders by Class	ifcb_zip_images_by_class
Create a Zip Archive of Manual MATLAB Files	ifcb_zip_matlab
Zip PNG Folders	ifcb_zip_pngs
Process IFCB String	process_ifcb_string
Function to Read Individual Files and Extract Relevant Lines	read_hdr_file
Split Large Zip File into Smaller Parts	split_large_zip
Summarize TreeBagger Classifier Results	summarize_TBclass
Convert Biovolume to Carbon for Diatoms (All Sizes)	vol2C_diatom
Convert Biovolume to Carbon for Large Diatoms	vol2C_lgdiatom
Convert Biovolume to Carbon for Non-Diatom Protists	vol2C_nondiatom

Package: iRfcb 0.9.0.9000

iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

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