zarrsmith.mosaic_manager.luxendo_mosaic_manager

Attributes

logger

Classes

LuxendoMosaicManager

Raw Luxendo tiles (*.lux.h5 + *.json) of one acquisition, before any fusion.

Module Contents

zarrsmith.mosaic_manager.luxendo_mosaic_manager.logger

class zarrsmith.mosaic_manager.luxendo_mosaic_manager.LuxendoMosaicManager(path, scan_workers: int = 16, progress: bool = True)

Bases: zarrsmith.mosaic_manager.mosaic.MosaicManager

Raw Luxendo tiles (*.lux.h5 + *.json) of one acquisition, before any fusion.

Not to be confused with LuxendoManager, which reads images already fused by the Luxendo software. This manager scans a raw acquisition folder such as 2026-10-14_103957 (tiles live in raw/<stack folder>/Cam_*.lux.h5) and exposes every tile lazily:

• channel: the dye, with the illumination side removed (autofluo-488-L and autofluo-488-R both give autofluo-488), so both halves of a sample end up in the same fused channel;

• group: the illumination side, "L" or "R" (used by blend="sigmoid" and "midline");

• timepoint: the JSON time_point, or the order of the acquisitions of a stack when the JSON has none;

• attrs: stack, stack_description, grid ((ix, iy)), channel_description and path.

Tile positions come from affine_to_sample in the JSON (the tile is centred on the stage translation in x/y; z is the plane position along the stacking direction). If a stack was re-acquired (*_R_<n>.lux.h5) only the latest retake is used. Tiles are H5Array objects, so no file stays open. Scanning reads only the JSON files (in parallel) and opens a single .h5 file, which keeps loading fast on network drives.

static _retake(h5: pathlib.Path) → int

Cam_bottom_00000.lux.h5 -> 0, Cam_bottom_00000_R_1.lux.h5 -> 1.

_scan() → List[zarrsmith.mosaic_manager.tile.Tile]

Discover the tiles under path (lazy data, positions in the sample frame).

scan_workers

progress = True

classmethod _acquisitions(folder) → List[pathlib.Path]

The *.lux.h5 acquisitions of a stack folder (those with a .json sibling).

Files sharing a base name are retakes (*_R_<n>) of one acquisition and only the latest is kept. Different base names are separate acquisitions of the same stack (e.g. timepoints); they are returned in name order.

static _read_info(h5: pathlib.Path) → dict

static _shape(info: dict) → tuple

classmethod _tile_from(h5: pathlib.Path, info: dict | None = None, dtype=None, default_timepoint: int = 0) → zarrsmith.mosaic_manager.tile.Tile

Tile of one .lux.h5 file; the file is only opened when dtype is not given.

The timepoint is the JSON time_point, or default_timepoint without one.