sample_preparation

This is the part that is common to both pipelines to process the raw images. It includes file conversion, stitching and registration

class PreProcessor

Bases: TabProcessor

Handle the stitching and alignment of the raw images

align(force=False)

check_has_all_tiles(channel)

Check whether all the tiles of the channel exist on disk

Parameters:

channel (str) – The channel to check

Returns

bool

True if all the tiles exist

clear_landmarks()

Clear (remove) the landmarks files

convert_tiles(force=False)

Convert list of input files to numpy files for efficiency reasons

Returns

convert_to_image_format()

Convert (optionally) to image formats readable by e.g. Fiji

delete_resampled_files()

filename(*args, **kwargs)

A shortcut to get the filename from the workspace

Parameters:

• args

• kwargs

Returns

str

The filename

get_atlas_files()

get_autofluo_pts_path(direction='resampled_to_auto')

Get the path to the autofluorescence landmarks file

Parameters:

direction

Returns

str

The path to the autofluorescence landmarks file

get_configs()

get_wobbly_layout(**kwargs)

overlay_layout_plane(layout)

Overlays the sources to check their placement.

Arguments

layoutLayout class

The layout with the sources to overlay.

Returns

imagearray

A color image.

static patch_elastix_cfg_landmarks(elastix_cfg_path)

Patches the elastix configuration file to use landmarks (CorrespondingPointsEuclideanDistanceMetric), in addition to AdvancedMattesMutualInformation

Warning

This method modifies the file in place and assumes that the existing

metric is AdvancedMattesMutualInformation

Parameters:

elastix_cfg_path (str) – Path to the elastix configuration file

plot_atlas()

plot_layout(postfix='aligned_axis')

plot_stitching_results(parent=None)

resample_for_registration(force=False)

static restore_elastix_cfg_no_landmarks(elastix_cfg_path)

Restores the elastix configuration file to not use landmarks (CorrespondingPointsEuclideanDistanceMetric), only AdvancedMattesMutualInformation

Warning

This method modifies the file in place and assumes that the existing metric is

AdvancedMattesMutualInformation

Parameters:

elastix_cfg_path

run()

set_configs(cfg_paths)

setup(cfgs, watcher=None, convert_tiles=True)

Parameters:

• (machine_cfg_path (cfgs tuple of) – (machine_cfg, sample_cfg, processing_cfg)

• sample_cfg_path – (machine_cfg, sample_cfg, processing_cfg)

• or (processing_cfg_path)) – (machine_cfg, sample_cfg, processing_cfg)

Returns

setup_atlases()

stack_columns()

stitch()

stitch_overlay(channel, color=True)

This creates a dumb overlay of the tiles i.e. only using the fixed guess overlap :param channel: :param color:

Returns

stitch_rigid(**kwargs)

stitch_wobbly(force=False)

unpack_atlas(atlas_base_name)

use_npy()

z_only(channel='raw')

Check if the channel is z only (no x or y tiles)

Parameters:

channel (str) – The channel to check

Returns

bool

True if the channel is z only

property aligned_autofluo_path

property autofluorescence_is_tiled

Check if the autofluorescence channel is tiled (has x and y tiles) .. rubric:: Returns

bool

True if the autofluorescence channel is tiled

property has_npy

Check if the raw channel is in npy format

Returns

bool

True if the raw channel is in npy format

property has_tiles

property is_tiled

Check if the raw channel is tiled (has x and y tiles)

Returns

bool

True if the raw channel is tiled

property n_channels

property n_channels_convert

property n_registration_steps

property n_rigid_steps_to_run

property n_wobbly_steps_to_run

property prefix

Get the prefix to use for the files

Returns

str

The prefix to use, None to not use any

property raw_stitched_shape

property ref_pts_path

property resampled_pts_path

property resampled_shape

property was_registered

property was_stitched_rigid

init_preprocessor(folder, atlas_base_name=None, convert_tiles=False)

main()