What's Changed

New features

• New function ifcb_classify_images() to classify one or more pre-extracted IFCB PNG images through a CNN model served by a Gradio application, returning a data frame of predicted class names and confidence scores. Per-class thresholds are applied automatically.
• New function ifcb_classify_sample() to classify all images in a raw IFCB sample (.roi file) without prior PNG extraction. Internally extracts images to a temporary directory and delegates to ifcb_classify_images().
• New function ifcb_save_classification() to classify IFCB samples via Gradio API and save results as HDF5 (.h5), MAT (.mat), or CSV (.csv) files.
• New function ifcb_classify_models() to list available CNN models from a Gradio classification server.
• Added HDF5 (.h5) and CSV (.csv) classification file support to ifcb_extract_biovolumes(), ifcb_extract_classified_images(), ifcb_summarize_class_counts(), ifcb_summarize_biovolumes(), and summarize_TBclass(), in addition to existing .mat support.

Breaking changes

• Image extraction functions (ifcb_extract_pngs(), ifcb_extract_annotated_images(), and ifcb_extract_classified_images()) now preserve raw pixel values by default (normalize = FALSE), producing images comparable to IFCB Dashboard and other standard IFCB software. Previously, pixel values were stretched to the full 0-255 range using min-max normalization. This change can affect classifier training results. Set normalize = TRUE to restore the previous behavior (#75).

Minor improvements and fixes

• ifcb_create_manual_file() now writes class2use_auto as a numeric matrix, matching the format produced by ifcb-analysis (#74).
• Corrected the parameter description of micron_factor in ifcb_psd() and ifcb_extract_biovolumes().
• Corrected the parameter description of skip_class in ifcb_extract_annotated_images().

Deprecations

• ifcb_run_image_gallery() is deprecated in favor of ClassiPyR::run_app(). See https://europeanifcbgroup.github.io/ClassiPyR/ for more information.
• Deprecated arguments:
  • old_adc in ifcb_extract_pngs(), ifcb_extract_annotated_images(), and ifcb_extract_classified_images(). ADC format (old IFCB1-6 vs new) is now auto-detected from the HDR file's ADCFileFormat parameter and the ADC column count.
  • mat_files in ifcb_extract_biovolumes() and ifcb_summarize_biovolumes() (replaced by class_files).
  • mat_recursive in ifcb_extract_biovolumes() and ifcb_summarize_biovolumes() (replaced by class_recursive).

Commits

• correct parameter description by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/73
• v.0.8.0 by @anderstorstensson in https://github.com/EuropeanIFCBGroup/iRfcb/pull/76

Full Changelog: https://github.com/EuropeanIFCBGroup/iRfcb/compare/0.7.0...0.8.0