ifcb_extract_annotated_images: Extract Annotated Images from IFCB Data

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

Extract Annotated Images from IFCB Data

Description

This function extracts labeled images from IFCB (Imaging FlowCytobot) data, annotated using the MATLAB code from the ifcb-analysis repository (Sosik and Olson 2007). It reads manually classified data, maps class indices to class names, and extracts the corresponding Region of Interest (ROI) images, saving them to the specified directory.

Usage

ifcb_extract_annotated_images(
  manual_folder,
  class2use_file,
  roi_folders,
  out_folder,
  skip_class = NA,
  verbose = TRUE,
  manual_recursive = FALSE,
  roi_recursive = TRUE,
  overwrite = FALSE,
  scale_bar_um = NULL,
  scale_micron_factor = 1/3.4,
  scale_bar_position = "bottomright",
  scale_bar_color = "black",
  old_adc = FALSE,
  use_python = FALSE,
  gamma = 1,
  normalize = FALSE,
  add_trailing_numbers = TRUE,
  roi_folder = deprecated()
)

Arguments

manual_folder	A character string specifying the path to the directory containing the manually classified .mat files.
class2use_file	A character string specifying the path to the file containing class names.
roi_folders	A character vector specifying one or more directories containing the ROI files.
out_folder	A character string specifying the output directory where the extracted images will be saved.
skip_class	A numeric vector of class IDs or a character vector of class names to be excluded from the .png extraction. Default is NA (include all classes).
verbose	A logical value indicating whether to print progress messages. Default is TRUE.
manual_recursive	Logical. If TRUE, the function will search for MATLAB files recursively within the manual_folder. Default is FALSE.
roi_recursive	Logical. If TRUE, the function will search for data files recursively within the roi_folders (if provided). Default is TRUE.
overwrite	A logical value indicating whether to overwrite existing PNG files. Default is FALSE.
scale_bar_um	An optional numeric value specifying the length of the scale bar in micrometers. If NULL, no scale bar is added.
scale_micron_factor	A numeric value defining the conversion factor from micrometers to pixels. Defaults to 1/3.4.
scale_bar_position	A character string specifying the position of the scale bar in the image. Options are "topright", "topleft", "bottomright", or "bottomleft". Defaults to "bottomright".
scale_bar_color	A character string specifying the scale bar color. Options are "black" or "white". Defaults to "black".
old_adc	Previously used to indicate old ADC format. ADC format is now auto-detected from the HDR file and column count. This parameter is ignored.
use_python	Logical. If TRUE, attempts to read the .mat file using a Python-based method. Default is FALSE.
gamma	A numeric value for gamma correction applied to the image. Default is 1 (no correction). Values <1 brighten dark regions, while values >1 darken the image.
normalize	A logical value indicating whether to apply min-max normalization to stretch pixel values to the full 0-255 range. Default is FALSE, preserving raw pixel values comparable to IFCB Dashboard output. See ifcb_extract_pngs() for details.
add_trailing_numbers	Logical. If TRUE, appends a zero-padded numeric suffix derived from the manual class index to the class name when naming output files. If FALSE, uses only the class name without a numeric suffix. Default is TRUE.
roi_folder	Use roi_folders instead.

Details

If use_python = TRUE, the function tries to read the .mat file using ifcb_read_mat(), which relies on SciPy. This approach may be faster than the default approach using R.matlab::readMat(), especially for large .mat files. To enable this functionality, ensure Python is properly configured with the required dependencies. You can initialize the Python environment and install necessary packages using ifcb_py_install().

If use_python = FALSE or if SciPy is not available, the function falls back to using R.matlab::readMat().

Value

None. The function saves the extracted PNG images to the specified output directory.

References

Sosik, H. M. and Olson, R. J. (2007), Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol. Oceanogr: Methods 5, 204–216.

See Also

ifcb_extract_pngs ifcb_extract_classified_images https://github.com/hsosik/ifcb-analysis

Examples

## Not run: 
ifcb_extract_annotated_images(
  manual_folder = "path/to/manual_folder",
  class2use_file = "path/to/class2use_file.mat",
  roi_folders = "path/to/roi_folder",
  out_folder = "path/to/out_folder",
  skip_class = 1 # Skip "unclassified"
)

## End(Not run)

iRfcb documentation built on March 1, 2026, 5:06 p.m.