Microscope Implementations

This module contains implementations of microscope-specific functionality.

ImageXpress

class ezstitcher.microscopes.imagexpress.ImageXpressFilenameParser

Filename parser for ImageXpress microscopes.

classmethod can_parse(cls, filename)

Check if this parser can parse the given filename.

Parameters:: filename (str) – Filename to check
Returns:: True if this parser can parse the filename, False otherwise
Return type:: bool

parse_filename(filename)

Parse an ImageXpress filename into its components.

Parameters:: filename (str) – Filename to parse
Returns:: Dictionary with extracted components or None if parsing fails
Return type:: dict or None

construct_filename(well, site=None, channel=None, z_index=None, extension='.tif', site_padding=3, z_padding=3)

Construct an ImageXpress filename from components.

Parameters:

well (str) – Well ID (e.g., ‘A01’)
site (int or str, optional) – Site number or placeholder string (e.g., ‘{iii}’)
channel (int, optional) – Channel/wavelength number
z_index (int or str, optional) – Z-index or placeholder string (e.g., ‘{zzz}’)
extension (str, optional) – File extension
site_padding (int, optional) – Width to pad site numbers to
z_padding (int, optional) – Width to pad Z-index numbers to

Returns:

Constructed filename

Return type:

str

class ezstitcher.microscopes.imagexpress.ImageXpressMetadataHandler

Metadata handler for ImageXpress microscopes.

find_metadata_file(plate_path)

Find the metadata file for an ImageXpress plate.

Parameters:: plate_path (str or Path) – Path to the plate folder
Returns:: Path to the metadata file, or None if not found
Return type:: Path or None

get_grid_dimensions(plate_path)

Get grid dimensions for stitching from ImageXpress metadata.

Parameters:: plate_path (str or Path) – Path to the plate folder
Returns:: Tuple of (grid_size_x, grid_size_y)
Return type:: tuple

get_pixel_size(plate_path)

Get the pixel size from ImageXpress metadata.

Parameters:: plate_path (str or Path) – Path to the plate folder
Returns:: Pixel size in micrometers, or None if not available
Return type:: float or None

Opera Phenix

class ezstitcher.microscopes.opera_phenix.OperaPhenixFilenameParser

Filename parser for Opera Phenix microscopes.

classmethod can_parse(cls, filename)

Check if this parser can parse the given filename.

Parameters:: filename (str) – Filename to check
Returns:: True if this parser can parse the filename, False otherwise
Return type:: bool

parse_filename(filename)

Parse an Opera Phenix filename into its components.

Parameters:: filename (str) – Filename to parse
Returns:: Dictionary with extracted components or None if parsing fails
Return type:: dict or None

construct_filename(well, site=None, channel=None, z_index=None, extension='.tiff', site_padding=1, z_padding=1)

Construct an Opera Phenix filename from components.

Parameters:

well (str) – Well ID (e.g., ‘A01’)
site (int or str, optional) – Site number or placeholder string (e.g., ‘{iii}’)
channel (int, optional) – Channel/wavelength number
z_index (int or str, optional) – Z-index or placeholder string (e.g., ‘{zzz}’)
extension (str, optional) – File extension
site_padding (int, optional) – Width to pad site numbers to
z_padding (int, optional) – Width to pad Z-index numbers to

Returns:

Constructed filename

Return type:

str

class ezstitcher.microscopes.opera_phenix.OperaPhenixMetadataHandler

Metadata handler for Opera Phenix microscopes.

find_metadata_file(plate_path)

Find the metadata file for an Opera Phenix plate.

Parameters:: plate_path (str or Path) – Path to the plate folder
Returns:: Path to the metadata file, or None if not found
Return type:: Path or None

get_grid_dimensions(plate_path)

Get grid dimensions for stitching from Opera Phenix metadata.

Parameters:: plate_path (str or Path) – Path to the plate folder
Returns:: Tuple of (grid_size_x, grid_size_y)
Return type:: tuple

get_pixel_size(plate_path)

Get the pixel size from Opera Phenix metadata.

Parameters:: plate_path (str or Path) – Path to the plate folder
Returns:: Pixel size in micrometers, or None if not available
Return type:: float or None