Readers and conventions

The microscope managers in zarrsmith.microscope_manager read a dataset and normalize it to one shared API.

The main reader classes currently exposed by zarrsmith.microscope_manager are:

  • ArrayManager — wrap an in-memory NumPy or Dask array using ZarrSmith metadata conventions.

  • LuxendoManager — Luxendo XML + HDF5 datasets.

  • OperaManager — Opera Phenix / Opera PE OME-TIFF style datasets.

  • ScapeManager — Leica SCAPE OME-TIFF + XLIF datasets.

  • ViventisManager — Viventis LS1 datasets.

  • ZeissManager — Zeiss CZI datasets.

  • EvidentManager — Olympus/Evident cellSens VSI datasets: the .vsi file plus its _<name>_/ folder of .ets pixel data, read with slideio. Tiled acquisitions are stored stitched and are read as one image; select a scene with scene_index or scene_name. The lower-resolution levels that cellSens stores for large images (downsampled in Y and X only) are exposed as extra pyramid levels, so the raw file renders quickly in napari 3D; pass native_levels=False to read the full resolution only. Single-tile acquisitions usually have no stored levels.

  • ZarrManager — NGFF v0.4/v0.5 OME-Zarr datasets.

  • ZarrV04Manager — compatibility reader for older v0.4-style datasets.

All file-based readers share the same conventions:

  • The dataset location is the first argument (path; for ScapeManager the OME-TIFF file) and chunks is an optional TCZYX tuple. When omitted, chunks defaults to the manager’s DEFAULT_CHUNKS ((1, 1, 8, 4096, 4096) for most readers, (1, 1, 8, 1024, 1024) for ScapeManager, (1, 1, 8, 2048, 2048) for EvidentManager, the native chunking for ZeissManager).

  • The dataset is read in the constructor, so .data (one lazy dask array per pyramid level) and .metadata are available immediately. read() returns None.

  • Managers can be used as context managers, which closes any open file handle (HDF5 files for LuxendoManager) on exit:

    with mm.LuxendoManager("path/to/luxendo_folder") as lux:
    lux.to_zarr("output.zarr")

  • The metadata uses one spelling everywhere: channel colors are RRGGBB hex strings (no #), spatial units are NGFF names such as "micrometer", and time units are e.g. "second".

  • Progress messages (opened scenes, subsets, metadata updates, the Zarr tree printed when opening a store) go through the standard logging module under the "zarrsmith" logger and are silent by default. Show them with:

    import logging
logging.basicConfig(format="%(message)s")
logging.getLogger("zarrsmith").setLevel(logging.INFO)

To support a new acquisition system, see Adding a microscope manager; for acquisitions saved as separate tiles, see Mosaics.