papylio.Experiment

class papylio.Experiment(*args, **kwargs)

__init__(*args, **kwargs)

Init method for the Experiment class

Loads config file if it locates one in the main directory, otherwise it exports the default config file to the main directory. Scans all directory in the main directory recursively and imports all found files (if import_all is set to True).

Parameters:

• main_path (str) – Absolute path to the main experiment folder

• channels (list of str) – Channels used in the experiment

• import_all (bool) – If true, then all files in the main folder are automatically imported.

  If false, then files are detected, but not imported.

Methods

__init__(*args, **kwargs)	Init method for the Experiment class
add_common_image_corrections_to_movies()	Apply common image corrections to all movie objects.
add_files(paths[, test_duplicates])	Find unique files in all subfolders and add them to the experiment
boxplot_number_of_molecules()	Boxplot of the number of molecules in each file
determine_flatfield_and_darkfield_corrections(files)	Determine and save flatfield and darkfield corrections for image shading.
export_number_of_molecules_per_file()	Export the number of molecules in each file to an Excel spreadsheet.
files_with_sequencing_match([files])
find_file_paths_and_extensions(paths)	Find unique files in all subfolders and add them to the experiment
generate_tile_mappings(files_for_mapping[, ...])
histogram([axis, bins, parameter, ...])	FRET histogram of all molecules in the experiment or a specified selection
import_sequencing_data(file_path[, ...])
import_sequencing_data_for_mapping(file_path)
import_sequencing_data_old()
load_darkfield_correction()	Load darkfield correction images from disk.
load_flatfield_correction()	Load flatfield correction images from disk.
plot_trace([files, query])	Plot molecule traces with interactive visualization.
print_files()	Print a summary of all files in the experiment.
select()	Simple method to look through all molecules in the experiment
sequencing_match_info_mean([distance_threshold])
sequencing_match_info_per_file()
sequencing_matches([files])
show_sequencing_matches([show_file_coordinates])
transform_sequencing_to_single_molecule_coordinates()

Attributes

analysis_path	Path to the Analysis folder.
channels	Channels used in the experiment.
file_paths	List of relative file paths for all files in experiment
mapping_file	Mapping file object from the experiment, if one exists.
nc_file_paths	List of relative NetCDF file paths for all files in experiment
number_of_channels	Number of channels used in the experiment (read-only)
pairs	List of channel pairs
selectedFiles	List of selected files
tile_mappings
tile_mappings_dict

add_common_image_corrections_to_movies()

Apply common image corrections to all movie objects.

Sets the common image corrections (flatfield, darkfield) to all movie objects in the experiment so they can be applied during image processing.

add_files(paths, test_duplicates=True)

Find unique files in all subfolders and add them to the experiment

Get all files in all subfolders of the main_path and remove their suffix (extensions), and add them to the experiment.

Note

Non-relevant files are excluded e.g. files with underscores or ‘Analysis’ in their name, or files with dat, db, ini, py and yml extensions.

Note

Since sifx files made using spooling are all called ‘Spooled files’ the parent folder is used as file instead of the sifx file

property analysis_path

Path to the Analysis folder.

Creates the Analysis folder in the main experiment directory if it does not exist, then returns the path.

Type:

pathlib.Path

boxplot_number_of_molecules()

Boxplot of the number of molecules in each file

property channels

Channels used in the experiment.

Setting the channels will automatically update pairs.

Type:

list of str

determine_flatfield_and_darkfield_corrections(files, method='BaSiC', illumination_index=0, frame_index=0, estimate_darkfield=True, **kwargs)

Determine and save flatfield and darkfield corrections for image shading.

Calculates spatial shading corrections using the specified method and saves them as TIFF files in the main experiment directory. Automatically loads the corrections into the experiment.

Parameters:

• files (FileCollection) – Collection of files to use for determining corrections

• method (str, optional) – Correction method to use (default: ‘BaSiC’)

• illumination_index (int, optional) – Index of the illumination pattern to correct (default: 0)

• frame_index (int, optional) – Frame index to use for correction calculation (default: 0)

• estimate_darkfield (bool, optional) – If True, also estimate and save darkfield correction (default: True)

• **kwargs – Additional keyword arguments passed to spatial_shading_correction

export_number_of_molecules_per_file()

Export the number of molecules in each file to an Excel spreadsheet.

Creates an Excel file containing a summary of the number of molecules detected in each file of the experiment. Missing files are marked with -1. The file is saved as ‘number_of_molecules.xlsx’ in the main experiment directory.

property file_paths

List of relative file paths for all files in experiment

Type:

list of pathlib.Path

files_with_sequencing_match(files=None)

find_file_paths_and_extensions(paths)

Find unique files in all subfolders and add them to the experiment

Get all files in all subfolders of the main_path and remove their suffix (extensions), and add them to the experiment.

Note

Non-relevant files are excluded e.g. files with underscores or ‘Analysis’ in their name, or files with dat, db, ini, py and yml extensions.

Note

Since sifx files made using spooling are all called ‘Spooled files’ the parent folder is used as file instead of the sifx file

generate_tile_mappings(files_for_mapping, mapping_sequence_name=None, surface=0, name='All files')

histogram(axis=None, bins=100, parameter='E', molecule_averaging=False, fileSelection=False, moleculeSelection=False, makeFit=False, export=False, **kwargs)

FRET histogram of all molecules in the experiment or a specified selection

Parameters:

• axis (matplotlib.axis) – Axis to use for histogram plotting

• bins (int) – Number of bins

• parameter (str) – Parameter to be used for histogram I or E

• molecule_averaging (bool) – If True an time average of the trace is used

• fileSelection (bool) – If True the histogram is made only using selected files.

• moleculeSelection (bool) – If True the histogram is made only using selected molecules.

• makeFit (bool) – If True perform Gaussian fitting.

• export (bool) – If True the graph is exported.

• **kwargs – Arbitrary keyword arguments.

import_sequencing_data(file_path, index1_file_path=None, remove_duplicates=True, add_aligned_sequence=True, extract_sequence_subset=False, chunksize=10000, store_relative_filepath=True)

import_sequencing_data_for_mapping(file_path, surface=0)

import_sequencing_data_old()

load_darkfield_correction()

Load darkfield correction images from disk.

Searches for darkfield correction TIFF files in the main experiment directory. If found, loads them and adds them to the common image corrections dataset. Updates all movie objects with the loaded corrections.

load_flatfield_correction()

Load flatfield correction images from disk.

Searches for flatfield correction TIFF files in the main experiment directory. If found, loads them and adds them to the common image corrections dataset. Updates all movie objects with the loaded corrections.

property mapping_file

Mapping file object from the experiment, if one exists.

Returns the first file marked as a mapping file. Returns None if no mapping file is found.

Type:

File

property nc_file_paths

List of relative NetCDF file paths for all files in experiment

Type:

list of pathlib.Path

property number_of_channels

Number of channels used in the experiment (read-only)

Type:

int

property pairs

List of channel pairs

Type:

list of list of str

plot_trace(files=None, query={}, **kwargs)

Plot molecule traces with interactive visualization.

Opens an interactive window to visualize and inspect molecule traces from NetCDF files. Allows filtering of molecules using a query.

Parameters:

• files (FileCollection, optional) – Files to plot traces from. If None, uses all files in experiment

• query (dict, optional) – Query dictionary to filter molecules (default: {})

• **kwargs – Additional keyword arguments passed to TracePlotWindow

print_files()

Print a summary of all files in the experiment.

Outputs a formatted representation of all files currently loaded in the experiment.

select()

Simple method to look through all molecules in the experiment

Plots a molecule. If enter is pressed the next molecule is shown.

property selectedFiles

List of selected files

Type:

list of File

sequencing_match_info_mean(distance_threshold=25)

sequencing_match_info_per_file()

sequencing_matches(files=None)

show_sequencing_matches(show_file_coordinates=False)

property tile_mappings

property tile_mappings_dict

transform_sequencing_to_single_molecule_coordinates()