microcorrelate.stitching#

This module contains functions for stitching together microscopy images

Classes#

`Length`	A physical length with lossless unit conversion.
`PixelSize`	Physical size of a single pixel.
`StagePosition`	Global stage coordinates of the top-left corner of a stitched tileset.
`TilesetMetadata`	Physical metadata of a Maps stitched tileset.

Functions#

stitch_images(→ None)

Stitch together tiled images from a tileset acquired via the Thermo Fisher Maps

Module Contents#

class microcorrelate.stitching.Length(meters: float)#

A physical length with lossless unit conversion.

Stores a length in metres as the canonical representation and exposes read-only properties for common unit conversions. Intended to eliminate scattered unit conversion factors across the stitching pipeline.

Parameters:: meters (float) – Length in metres.

Examples

l = Length(1.5e-7)
l.m   # 1.5e-07
l.um  # 0.15
l.nm  # 150.0

property cm: float#

property m: float#

property mm: float#

property nm: float#

property um: float#

class microcorrelate.stitching.PixelSize#

Physical size of a single pixel.

Parameters:

y (Length) – Pixel size along the Y axis.
x (Length) – Pixel size along the X axis.

Examples

pixel_size = PixelSize(y=Length(1.5e-7), x=Length(1.5e-7))
pixel_size.y.nm  # 150.0
pixel_size.x.um  # 0.15

class microcorrelate.stitching.StagePosition#

Global stage coordinates of the top-left corner of a stitched tileset.

Coordinates are extracted from MapsProject.xml and converted from the center-based convention used by Maps to top-left, so that pixel-to-physical coordinate mapping is a direct offset from index [0, 0]. Units in the MapsProject.xml are assumed to be meters.

Parameters:

y (Length) – Stage Y coordinate of the top-left corner.
x (Length) – Stage X coordinate of the top-left corner.

Examples

stage = StagePosition(y=Length(-0.020), x=Length(-0.011))
stage.x.um  # -11000.0
stage.y.nm  # -20000000.0

class microcorrelate.stitching.TilesetMetadata#

Physical metadata of a Maps stitched tileset.

Aggregates pixel size and optional stage position into a single object returned by _get_metadata. Stage position is None when MapsProject.xml is unavailable or the tileset cannot be matched.

Parameters:

pixel_size (PixelSize) – Physical size of a single pixel.
stage_position (StagePosition or None) – Global stage coordinates of the top-left corner, or None if unavailable.

microcorrelate.stitching.stitch_images(tileset_path: pathlib.Path | str, dest_path: pathlib.Path | str, compression: bool = True, group_path: str | None = None, pyramid_levels: int = 1, crop_borders: bool = True, verbose: bool = False) → None#

Stitch together tiled images from a tileset acquired via the Thermo Fisher Maps software and save the stitched image as a single TIFF file or Zarr file. The tileset is expected to be in the directory structure produced by Maps, and have been already stitched by the acquisition software (that is, there’s no overlap or gaps between tiles).

Parameters:

tileset_path (Path | str) – Path to the tileset directory.
dest_path (Path | str) – Path to save the stitched image. It can be either a .tif file or a .zarr store.
compression (bool) – Save Tiff image with compression (zlib). This parameter is only used when output is TIff. Zarr files are always compressed. (default = True).
group_path (str | None) – Path to the group in the Zarr array where images should be saved. If None, save in root. This parameter is only used if output is Zarr. (default = None).
pyramid_levels (int) – Number or pyramid levels used when saving to Zarr multiscales. If 1, no downscaled levels are calculated. (default = 1).
crop_borders (bool) – Crop black borders in the stitched dataset, which normally arise from a mismatch in the tile size and image size used by Maps. Note that this will briefly cause two copies of the image array to be held in memory, it should be used with caution when operating close to memory limits. (default = True).
verbose (bool) – Enable verbose output (default = False).

Return type:

None