ifcb_classify_sample: Classify All Images in an IFCB Sample Using a Gradio...

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

Classify All Images in an IFCB Sample Using a Gradio Application

Description

Extracts PNG images from an IFCB sample (.roi file) using ifcb_extract_pngs() into a temporary directory, then classifies each image through a CNN model served by a Gradio application. Per-class F2 optimal thresholds are applied automatically. The temporary directory is automatically removed when the function exits.

Usage

ifcb_classify_sample(
  roi_file,
  gradio_url = "https://irfcb-classify.hf.space",
  top_n = 1,
  model_name = "SMHI NIVA ResNet50 V5",
  verbose = TRUE,
  ...
)

Arguments

roi_file	A character string specifying the path to the .roi file.
gradio_url	A character string specifying the base URL of the Gradio application. Default is "https://irfcb-classify.hf.space", which is an example Hugging Face Space with limited resources intended for testing and demonstration. For large-scale classification, deploy your own instance of the classification app (source code: https://github.com/EuropeanIFCBGroup/ifcb-inference-app) and pass its URL here.
top_n	An integer specifying the number of top predictions to return per image. Default is 1 (top prediction only). Use Inf to return all predictions.
model_name	A character string specifying the name of the CNN model to use for classification. Default is "SMHI NIVA ResNet50 V5". Use ifcb_classify_models() to list all available models.
verbose	A logical value indicating whether to print progress messages. Default is TRUE.
...	Additional arguments passed to ifcb_extract_pngs() (e.g. ROInumbers, gamma, scale_bar_um).

Details

To classify individual pre-extracted PNG files, use ifcb_classify_images() directly.

Value

A data frame with the following columns:

file_name

The PNG file name of the classified image.

class_name

The predicted class name with per-class thresholds applied; "unclassified" if the score is below the threshold.

class_name_auto

The winning class name without any threshold applied (argmax of scores).

score

The prediction confidence score (0–1).

model_name

The name of the CNN model used for classification.

Images that could not be classified have NA in class_name, class_name_auto, and score. When top_n > 1, multiple rows are returned per image (one per prediction).

See Also

ifcb_classify_images() to classify pre-extracted PNG files directly. ifcb_classify_models() to list available CNN models. ifcb_extract_pngs() to extract PNG images from IFCB ROI files.

Examples

## Not run: 
# Classify all ROIs in a sample (top prediction per image)
result <- ifcb_classify_sample("path/to/D20220522T003051_IFCB134.roi")
head(result)

# Return top 3 predictions per image
result <- ifcb_classify_sample(
  "path/to/D20220522T003051_IFCB134.roi",
  top_n = 3
)

# Classify only specific ROI numbers
result <- ifcb_classify_sample(
  "path/to/D20220522T003051_IFCB134.roi",
  ROInumbers = c(1, 5, 10)
)

## End(Not run)

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