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Data & File Formats

SenoQuant uses BioIO with multiple format-specific plugins for faster pixel loading (for example bioio-czi, bioio-lif, bioio-nd2, bioio-ome-tiff, and bioio-ome-zarr). When possible, SenoQuant still opens metadata through bioio-bioformats to preserve richer metadata coverage from BioFormats.

Reader behavior

When you open a file in napari with SenoQuant installed:

  1. Data reader selection: SenoQuant prefers fast format-specific BioIO readers for pixel data, and falls back when needed.
  2. Metadata reader selection: SenoQuant tries to read metadata with bioio-bioformats whenever possible.
  3. Scene processing: Multi-scene files (e.g., .lif, .czi) have each scene loaded as separate layers.
  4. Channel splitting: Each channel within a scene becomes an individual image layer in napari.
  5. Colormap detection: Channel colors from OME metadata are used when available; otherwise falls back to a default colormap cycle.
  6. Metadata preservation: Physical pixel sizes, scene names, channel information, file path, etc., are stored in layer metadata.

Channel colormaps

OME metadata colors

When OME metadata is present in the image file, SenoQuant extracts channel colors and applies them as custom colormaps:

  • Each channel gets a colormap ranging from black to its specified color.
  • If all channels have the same color (e.g., all "white"), falls back to the default colormap cycle.

Default colormap cycle

When OME colors are not available or all channels share the same color, channels are assigned colormaps from a predefined cycle:

  • blue, green, red, yellow, cyan, bop blue, bop orange, bop purple

Scenes and channels

Multi-scene files

Files with multiple scenes (e.g., Leica .lif, Zeiss .czi) are processed as follows:

  • Each scene is loaded as a separate set of layers.
  • Layer names include the scene identifier (e.g., image.lif - Scene 1).
  • Scene metadata is accessible in the layer properties.

Channel organization

  • Each channel becomes a dedicated image layer.
  • Layer names include resolved channel names (for example, image.tif - DAPI).
  • Channel names prefer metadata-reader values and fall back to data-reader names when metadata names are generic placeholders (such as Channel:0:0).
  • Missing or blank names fall back to Channel {index}.
  • Blending mode is set to "additive" for multi-channel visualization.

Supported file formats

SenoQuant supports most common microscopy formats through BioIO plugins (with BioFormats metadata fallback), including:

  • Zeiss CZI: .czi
  • Leica LIF: .lif
  • Nikon ND2: .nd2
  • OME-TIFF: .ome.tiff, .ome.tif, .ome.tf2, .ome.tf8, .ome.btf
  • OME-ZARR: .zarr
  • TIFF: .tiff, .tif, .tf2, .tf8, .btf
  • PNG/JPEG: .png, .jpg
  • And many more: See the BioFormats supported formats list.

Note: If you have a file that SenoQuant cannot open, please submit an issue on GitHub with the file format and sample data if possible, and we will work on adding support.

Metadata accessibility

Layer metadata includes:

  • bioio_metadata: Full BioIO metadata structure.
  • scene_info: Scene identifier, index, and total scene count.
  • path: Original file path.
  • channel_index: Zero-based channel index.
  • channel_names: Resolved channel-name list for the active scene.
  • physical_pixel_sizes: Physical dimensions in micrometers (X, Y, Z).
  • data_reader: Reader class used for pixel data loading.
  • metadata_reader: Reader class used for metadata extraction.

Access metadata programmatically:

layer = viewer.layers["image.tif - DAPI"]
metadata = layer.metadata
scene_name = metadata["scene_info"]["scene_name"]
pixel_size_x = metadata["physical_pixel_sizes"]["X"]
all_channel_names = metadata["channel_names"]

Dimensionality

SenoQuant supports:

  • 2D images: Single Z-plane (YX data).
  • 3D images: Z-stacks (ZYX data).
  • Multi-channel: Any number of channels per scene.

Fallback readers

If SenoQuant cannot open your file:

  1. napari automatically tries other installed readers.
  2. Use napari's built-in readers, or install plugins from napari's Plugin Manager as alternatives.

Warning: Metadata-based quantification features (e.g., ones associated with physical units) will not work correctly if the SenoQuant reader is bypassed.