NEWS

bgnormR 0.99.3

read_qptiff() now auto-detects and reads OME-TIFF and OME-Zarr (OME-NGFF) images in addition to QPTIFF. OME-TIFF channel names are read from the <Channel Name="..."> attributes of the OME-XML; OME-Zarr stores are read (lazily, via a new OMEZarrArraySeed DelayedArray backend) using the optional Rarr package, with channel names and colours taken from omero.channels.
Image metadata is now returned as a QPTIFFMetadata object - an OME-organised hierarchy (slide / images[] -> image_info / channels[] / scales[]) - with accessors qpi_format(), qpi_channels(), qpi_channel_names(), qpi_pixel_size_um(), qpi_n_levels(), qpi_is_brightfield(), and a tidy channel_table().
write_qptiff() now emits richer OME-TIFF metadata - physical pixel size, per-channel fluorophore / colour / emission & excitation wavelengths, per-channel exposure <Plane> elements, and a qpi://vectra MapAnnotation carrying PerkinElmer-specific fields - so a read -> write -> read round trip preserves this metadata. Files continue to declare SizeC channels (with SizeZ = SizeT = 1) so viewers such as QuPath read the pages as channels rather than Z/T slices.

plot_qptiff() and plot_pixel_classes() now render plot titles, subtitles, and captions in white so they are legible on the dark image background, across both the QPTIFFImage raster and SpatialExperiment scatter render paths.

Added bgnorm_pixels() for pixel-level background normalisation of QPTIFFImage objects, supporting parallel channel processing via BiocParallel.
Added bgnorm_cells() and bgnorm_sce() for cell-level normalisation of SummarizedExperiment (including SingleCellExperiment and SpatialExperiment) objects.
Added QPTIFFImage S3 class (3-D array [H × W × C]) and as.QPTIFFImage() coercion generic.
Added read_qptiff() for reading Akoya PhenoCycler-Fusion QPTIFF images without Java.
Added QPTIFFArraySeed / DelayedArray backend for out-of-core lazy loading of QPTIFF images.
Added unified plotting functions: plot_qptiff(), plot_pixel_classes(), plot_distributions(), plot_jsd_heatmap() supporting both QPTIFFImage (raster) and SpatialExperiment (scatter) input.
Added jsd_qc() and qc_summary() for Jensen-Shannon Divergence quality control.
Added log_transform(), inv_log_transform(), and median_filter_3x3() pre-processing utilities.