ifcb_extract_pngs: Extract Images from IFCB ROI File

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

Extract Images from IFCB ROI File

Description

This function reads an IFCB (.roi) file and its corresponding .adc file, extracts regions of interest (ROIs), and saves each ROI as a PNG image in a specified directory. Optionally, you can specify ROI numbers to extract, useful for specific ROIs from manual or automatic classification results. Additionally, a scale bar can be added to the extracted images based on a specified micron-to-pixel conversion factor.

Usage

ifcb_extract_pngs(
  roi_file,
  out_folder = dirname(roi_file),
  ROInumbers = NULL,
  taxaname = NULL,
  gamma = 1,
  normalize = FALSE,
  overwrite = FALSE,
  scale_bar_um = NULL,
  scale_micron_factor = 1/3.4,
  scale_bar_position = "bottomright",
  scale_bar_color = "black",
  old_adc = FALSE,
  verbose = TRUE
)

Arguments

roi_file	A character string specifying the path to the .roi file.
out_folder	A character string specifying the directory where the PNG images will be saved. Defaults to the directory of the ROI file.
ROInumbers	An optional numeric vector specifying the ROI numbers to extract. If NULL, all ROIs with valid dimensions are extracted.
taxaname	An optional character string specifying the taxa name for organizing images into subdirectories. Defaults to NULL.
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, which preserves raw pixel values from the camera, producing images comparable to IFCB Dashboard and other standard IFCB software. Set to TRUE to stretch contrast to the full 0-255 range.
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.
verbose	A logical value indicating whether to print progress messages. Default is TRUE.

Value

This function is called for its side effects: it writes PNG images to a directory.

See Also

ifcb_extract_classified_images for extracting ROIs from automatic classification.

ifcb_extract_annotated_images for extracting ROIs from manual annotation.

Examples

## Not run: 
# Convert ROI file to PNG images
ifcb_extract_pngs("path/to/your_roi_file.roi")

# Extract specific ROI numbers from ROI file
ifcb_extract_pngs("path/to/your_roi_file.roi", "output_directory", ROInumbers = c(1, 2, 3))

# Extract images with a 5 micrometer scale bar
ifcb_extract_pngs("path/to/your_roi_file.roi", scale_bar_um = 5)

## End(Not run)

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