zarrsmith.mosaic_manager.zeiss_mosaic_manager

Attributes

logger
_PIXEL_TYPES
_FOCUS

Classes

ZeissMosaicManager

Raw Zeiss tiles of one .czi file (a ZEN tile scan), before any stitching.

Functions

scene_names(czi_metadata) → Dict[int, str]	{scene index: name} of a CZI file (names may be missing).
channel_names(czi_metadata, indices) → Dict[int, str]	{channel index: name} for indices, unique so that channels are not fused together.
field_name(scene, name) → str	scene0_TR1: the index keeps the acquisition order and spaces are not allowed

Module Contents

zarrsmith.mosaic_manager.zeiss_mosaic_manager.logger

zarrsmith.mosaic_manager.zeiss_mosaic_manager._PIXEL_TYPES

zarrsmith.mosaic_manager.zeiss_mosaic_manager._FOCUS

zarrsmith.mosaic_manager.zeiss_mosaic_manager.scene_names(czi_metadata) → Dict[int, str]

{scene index: name} of a CZI file (names may be missing).

zarrsmith.mosaic_manager.zeiss_mosaic_manager.channel_names(czi_metadata, indices) → Dict[int, str]

{channel index: name} for indices, unique so that channels are not fused together.

zarrsmith.mosaic_manager.zeiss_mosaic_manager.field_name(scene: int, name: str | None) → str

scene0_TR1: the index keeps the acquisition order and spaces are not allowed in field names, which the command line and batch CSV separate with spaces.

class zarrsmith.mosaic_manager.zeiss_mosaic_manager.ZeissMosaicManager(path, scene_index: int | None = None)

Bases: zarrsmith.mosaic_manager.mosaic.MosaicManager

Raw Zeiss tiles of one .czi file (a ZEN tile scan), before any stitching.

Not to be confused with ZeissManager, which reads one scene as a single image; a file without tiles, such as the output of ZEN’s Stitching, is read with it. Every tile (M index) of every channel and timepoint is one tile, and its planes stay on disk until read (CziTileArray).

• channel: the channel name in the metadata (AF488-T2);

• field: the scene: scene0_TR1, scene1_P1, … with the tile regions and positions of the ZEN experiment as TR1 and P1;

• timepoint: the T index;

• attrs: stack (scene0_TR1-m00, the tile id without the channel), scene, scene_name, mosaic_index and path.

Tiles are placed where the file says: y and x from the pixel coordinates of the tile in the file (the stage position, rounded to a pixel), z from the FocusPosition of its first plane. They are not registered, unlike the images stitched by ZEN. Positions in the file change a little between timepoints: by default a fusion uses those of one reference timepoint, as ZEN uses one offset for all; reference_timepoint="all" uses those of every timepoint.

scene_index = None

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

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

static _stacks(czi) → Dict[Tuple, dict]

{(scene, m, t, c): {"coords": ..., "boxes": {z: box}}}, from the directory of the file.

static _focus_positions(czi, z: int, c: int) → Dict[Tuple, float]

{(scene, m, t): focus position (um)} of plane z of channel c (one read per tile).