megafish.load module

make_dirlist(dirlist_path, image_dir)[source]

Generates a CSV file listing all cycle directories within a specified image directory. Each cycle directory must contain tiled images organized by color, z, y, and x.

Parameters:

dirlist_path (str) – The file path to save the generated directory list CSV.
image_dir (str) – The path to the main directory containing subfolders for each cycle.

Returns:

The function creates a CSV file at dirlist_path.

Return type:

None

make_imagepath_cYX_from_dirlist(zarr_path, groups, channels, n_cycle, n_tile_y, n_tile_x, scan_type, dirlist_path, subfooter='', footer='_imagepath', ext='.tif')[source]

Generates a CSV file mapping image paths to cycle, tile, and channel information for spatial-omics images.

Parameters:

zarr_path (str) – Path to the base .zarr file.
groups (list of str) – List of group names, each corresponding to a specific analysis group.
channels (list of str) – List of channels corresponding to the groups.
n_cycle (int) – Total number of cycles to process.
n_tile_y (int) – Number of tiles along the y-axis.
n_tile_x (int) – Number of tiles along the x-axis.
scan_type (str) – Type of scan, determining the tile layout.
dirlist_path (str) – Path to the CSV file with the list of cycle directories.
subfooter (str, optional) – String to append before the footer in the output CSV filename; defaults to an empty string.
footer (str, optional) – String appended to the output CSV filename; defaults to “_imagepath”.
ext (str, optional) – File extension of the image files; defaults to “.tif”.

Returns:

The function creates a CSV file with the generated image paths and associated metadata at the modified zarr_path.

Return type:

None

make_imagepath_cYX(zarr_path, groups, channels, n_cycle, n_tile_y, n_tile_x, scan_type, image_dir, subfooter='', footer='_imagepath', ext='.ims')[source]

Generates a CSV file mapping image paths to cycle, tile, and channel information for spatial-omics data.

Parameters:

zarr_path (str) – Path to the base .zarr file.
groups (list of str) – List of group names, each corresponding to a specific analysis group.
channels (list of str) – List of channels corresponding to the groups.
n_cycle (int) – Total number of cycles to process.
n_tile_y (int) – Number of tiles along the y-axis.
n_tile_x (int) – Number of tiles along the x-axis.
scan_type (str) – Type of scan, determining the tile layout.
image_dir (str) – Path to the main directory containing subfolders for each cycle, each with images organized by color, z, y, and x.
subfooter (str, optional) – String to append before the footer in the output CSV filename; defaults to an empty string.
footer (str, optional) – String appended to the output CSV filename; defaults to “_imagepath”.

Returns:

The function creates a CSV file with image paths and associated metadata at the modified zarr_path.

Return type:

None

ims_cYXzyx(zarr_path, n_z, n_y, n_x, imagepath_footer='_imagepath')[source]

Creates empty Zarr arrays for image data in cycle, tile, and spatial (z, y, x) dimensions, then loads .ims images into these arrays using metadata from an image path CSV.

Parameters:

zarr_path (str) – Path to the base .zarr file to store image data.
n_z (int) – Number of z-slices per tile.
n_y (int) – Image height (pixels) for each tile.
n_x (int) – Image width (pixels) for each tile.
imagepath_footer (str, optional) – String to append to the CSV filename; defaults to “_imagepath”.

Returns:

The function creates Zarr arrays with image data and writes to zarr_path.

Return type:

None

tif_cYXzyx(zarr_path, n_z, n_y, n_x, imagepath_footer='_imagepath', ext='.tif', dtype=None, tif_dims='czyx')[source]

Creates empty Zarr arrays for image data in cycle, tile, and spatial (z, y, x) dimensions, then loads TIFF images into these arrays using metadata from an image path CSV.

Parameters:

zarr_path (str) – Path to the base .zarr file to store image data.
n_z (int) – Number of z-slices per tile.
n_y (int) – Image height (pixels) for each tile.
n_x (int) – Image width (pixels) for each tile.
imagepath_footer (str, optional) – String to append to the CSV filename; defaults to “_imagepath”.
ext (str, optional) – File extension of the image files; defaults to “.tif”.
dtype (str, optional) – Data type to cast the image to; defaults to None.
dims (str, optional) – Order of dimensions in the image data; defaults to “czyx”.

Returns:

The function creates Zarr arrays with image data and writes to zarr_path.

Return type:

None

stitched_ims(zarr_path, group, image_path, channel, n_tile_y, n_tile_x)[source]

Processes a stitched image by splitting it into tiles and saving them in a Zarr array.

Parameters:

zarr_path (str) – Path to the Zarr file where tiled data will be saved.
group (str) – Group name in the Zarr file for storing the tiled image data.
image_path (str) – Path to the stitched image file in .ims format.
channel (int) – Channel index for selecting specific image data.
n_tile_y (int) – Number of tiles along the y-axis.
n_tile_x (int) – Number of tiles along the x-axis.

Returns:

The function saves tiled images in the specified Zarr group without returning any value.

Return type:

None

stitched_tif(zarr_path, group, image_path, n_tile_y, n_tile_x, dtype='uint16')[source]

Processes a stitched TIFF image by splitting it into tiles and saving them in a Zarr array.

Parameters:

zarr_path (str) – Path to the Zarr file where tiled data will be saved.
group (str) – Group name in the Zarr file for storing the tiled image data.
image_path (str) – Path to the stitched image file in TIFF format.
n_tile_y (int) – Number of tiles along the y-axis.
n_tile_x (int) – Number of tiles along the x-axis.
dtype (str, optional) – Data type to cast the image to; defaults to “uint16”.

Returns:

The function saves tiled images in the specified Zarr group without returning any value.

Return type:

None