|
Zarr.NET
0.6.1
Zarr reader and writer in .NET
|
| ▼NZarrNET | |
| ▼NCore | |
| ▼NHelpers | |
| CPlaneResult | Result of reading a 2D plane. Provides convenience methods for extracting the actual 2D array and metadata about which axes were selected |
| ▼NNodes | |
| CBioformats2RawCollectionNode | A bioformats2raw.layout wrapper group containing one or more image series. Analogous to a PlateNode — it's a container you navigate into |
| CFieldNode | A single field (image acquisition) within a well. Behaves like a MultiscaleNode — has resolution levels and optionally labels |
| CLabelGroupNode | The "labels" sub-group of a multiscale image. Lists available label arrays |
| CLabelNode | A single named label array with its own multiscale pyramid. Semantically identical to a MultiscaleNode but carries additional label-specific metadata (colors, properties, source link) |
| CMultiscaleNode | Represents a multiscale image group. Contains one or more resolution levels and optionally a labels sub-group |
| COmeZarrNode | Base class for all OME-Zarr navigable nodes. Carries the underlying ZarrGroup and the detected node type |
| CPlateNode | Root node for an HCS (High-Content Screening) plate. Provides navigation to rows, columns, and individual wells |
| CResolutionLevelNode | A single resolution level within a multiscale image. This is the leaf node that provides actual data access |
| CWellNode | A single well within an HCS plate. Contains one or more fields (image acquisitions) |
| ▼NOmeZarr | |
| ▼NCoordinates | |
| CCoordinateTransformService | Converts between physical coordinate space (ROI in microns, etc.) and array index space (PixelRegion) using the coordinate transformations declared in OME-Zarr metadata |
| CPhysicalROI | A region of interest expressed in physical units (e.g. micrometers). Axis order matches the multiscale axes declaration. All values are axis-aligned (no rotation) |
| CPixelRegion | A region expressed in pixel (array index) coordinates. Maps directly to ZarrArray.ReadRegionAsync parameters |
| ▼NMetadata | |
| CAcquisitionMetadata | |
| CAxisMetadata | A single axis in an OME-Zarr multiscale image |
| CBioformats2RawMetadata | Metadata for a bioformats2raw.layout wrapper group. The wrapper contains numbered sub-groups (0, 1, 2, ...) each holding a multiscale image, and optionally an OME sub-group with a series index and METADATA.ome.xml |
| CChannelDisplayMetadata | |
| CColumnMetadata | |
| CCoordinateTransformation | A coordinate transformation that maps from array index space to physical space. May be a scale, translation, or identity |
| CDatasetMetadata | One resolution level (dataset) within a multiscale image. Path is relative to the multiscale group, e.g. "0", "1", "2" |
| CFieldCount | |
| CFieldReference | Reference to a field (image) within a well |
| CImageLabelMetadata | Metadata for a single label array. The array itself has multiscale metadata just like an image, with an additional "image-label" attribute |
| CLabelColorEntry | |
| CLabelGroupMetadata | Label group metadata. Lives in the "labels" sub-group's attributes. Lists the names of label arrays available under this group |
| CLabelProperty | |
| CLabelSourceLink | |
| CMultiscaleMetadata | Parsed "multiscales" entry from the OME-Zarr attributes object. A single zarr.json attributes block may declare one or more multiscale images, though in practice there is almost always exactly one |
| COmeMetadata | Optional rendering metadata from Omero, carried in the multiscale attributes. Used for display hints: channel colours, contrast limits, etc |
| COmeXmlChannelMetadata | Metadata for a single Channel element within an Image's Pixels |
| COmeXmlDetectorMetadata | |
| COmeXmlImageMetadata | Metadata for a single Image element in OME-XML. Corresponds to one series in the bioformats2raw layout |
| COmeXmlInstrumentMetadata | Metadata for an Instrument element in OME-XML. Contains the microscope, objectives, and detectors used for acquisition |
| COmeXmlMetadata | Top-level container for metadata parsed from METADATA.ome.xml. Contains all images (series) and instruments defined in the XML |
| COmeXmlObjectiveMetadata | |
| CPlateMetadata | Top-level plate metadata for HCS (High-Content Screening) data. Lives in the root group's attributes under the "plate" key |
| CRenderingWindowMetadata | |
| CRowMetadata | |
| CWellMetadata | Well metadata. Lives in each well group's attributes under the "well" key. Lists all fields (acquisitions/images) within the well |
| CWellReference | Reference to a well within a plate, linking row/column names to a path |
| CWindowMetadata | |
| ▼NZarr | |
| ▼NStore | |
| CChunkLruCache | Thread-safe LRU cache for decoded chunk data, keyed by chunk path |
| CHttpZarrStore | IZarrStore implementation for reading Zarr datasets over HTTP/HTTPS. Supports public S3 buckets, Azure Blob Storage, Google Cloud Storage, and any HTTP server serving Zarr files |
| CIZarrStore | Pure key/value store abstraction. Keys are forward-slash-separated paths relative to the store root (e.g. "0/0.0.0", "labels/nuclei/zarr.json"). No Zarr semantics live here — this is infrastructure only |
| CLocalFileSystemStore | IZarrStore backed by the local filesystem. Keys map directly to relative paths under the root directory, using the OS path separator |
| CS3ZarrStore | IZarrStore implementation backed by the AWS S3 SDK |
| CZarrArray | Represents a single Zarr v3 array. Knows how to read and write chunks via the store using the array's codec pipeline and chunk key encoding |
| CZarrGroup | Represents a Zarr v3 group node. Provides navigation to child groups and arrays by reading zarr.json entries from the store |
| CBioImageDescriptor | Everything the writer needs to know about a 5D image being saved. Shape is always interpreted as (T, C, Z, Y, X) in this descriptor. All dimension sizes must be at least 1 |
| COmeZarrReader | Entry point for reading OME-Zarr datasets |
| COmeZarrWriter | Creates a new OME-Zarr v3 dataset on disk and writes pixel data into it |
| CResolutionLevelDescriptor | Describes one resolution level in a multi-scale pyramid |
| CZCT | |
| CBloscCodec | Blosc bytes-to-bytes codec |
| CBytesCodec | The "bytes" array-to-bytes codec (Zarr v3 spec section 3.3.2). Handles endianness conversion when translating between the in-memory array representation and a flat byte sequence. This is always the first codec in a Zarr v3 pipeline |
| CChunkGridConfigurationDocument | |
| CChunkGridDocument | |
| CChunkKeyEncodingConfigurationDocument | |
| CChunkKeyEncodingDocument | |
| CCodecDocument | |
| CCodecPipeline | Applies an ordered list of codecs as a pipeline |
| CCrc32cCodec | The "crc32c" bytes-to-bytes codec (Zarr v3 spec) |
| CGzipCodec | Gzip bytes-to-bytes codec. Wraps System.IO.Compression — no native dependencies. Configuration mirrors the zarr.json "gzip" codec configuration object |
| CIZarrCodec | A single step in a Zarr v3 codec pipeline. Codecs are applied in order during encoding (array → bytes → compressed) and reversed during decoding. Each codec is responsible for one transformation only |
| CReader | |
| CShardingConfig | Configuration for a sharding_indexed codec parsed from zarr.json |
| CZarrArrayMetadata | Typed metadata for a Zarr array node. Knows everything needed to read/write chunks — shape, data type, chunk layout, codec pipeline configuration. No OME-Zarr knowledge here |
| CZarrDataType | Typed representation of a Zarr v3 data type string (e.g. "uint8", "float32"). Resolves element size in bytes and provides type classification used by the codec pipeline for byte-order handling |
| CZarrGroupMetadata | Typed metadata for a Zarr v3 group node. Groups are pure containers — no data, no shape, just attributes and children |
| CZarrJsonDocument | Raw deserialisation of a zarr.json node document (Zarr v3 spec). This is the only place we touch raw JSON — all higher layers work with typed metadata objects derived from this |
| CZarrV2ArrayDocument | Raw deserialization of a .zarray file (Zarr v2). Maps array metadata — shape, chunks, dtype, compression |
| CZarrV2AttrsDocument | Raw deserialization of a .zattrs file (Zarr v2). This is freeform JSON — OME-Zarr metadata lives here. We just parse it as a raw JsonElement and pass to OmeAttributesParser |
| CZarrV2CompressorDocument | |
| CZarrV2GroupDocument | Raw deserialization of a .zgroup file (Zarr v2). Just contains the format version — no other metadata |
| CZstdCodec | Zstandard bytes-to-bytes codec. Uses ZstdSharp (managed wrapper around the native zstd library, available as a NuGet package). NuGet: ZstdSharp.Port (pure managed port, no native deps) |