Welcome to pythologist-reader’s documentation!¶

Modules¶

class pythologist_reader.CellProjectGeneric(h5path, mode='r')[source]¶

append_sample(sample)[source]¶

Append sample to the project

Parameters: sample (CellSampleGeneric) – sample object

property cdf¶: Return the pythologist.CellDataFrame of the project

property channel_image_dataframe¶: dataframe within info about channels and images

frame_iter()[source]¶: An interator of CellFrameGeneric

get_image(sample_id, frame_id, image_id)[source]¶

Get an image by sample frame and image id

Parameters

sample_id (str) – unique sample id
frame_id (str) – unique frame id
image_id (str) – unique image id

Returns

2d image array

Return type

numpy.array

get_sample(sample_id)[source]¶

Get the sample_id

Parameters: sample_id (str) – set the sample id

property id¶: Returns the (str) UUID4 string

property key¶: Get info about the project

property microns_per_pixel¶: Return or set the (float) microns_per_pixel

property project_name¶: Return or set the (str) project_name

qc(*args, **kwargs)[source]¶

Returns: QC class to do quality checks
Return type: QC

property sample_ids¶: Return the list of sample_ids

sample_iter()[source]¶: An interator of CellSampleGeneric

set_id(name)[source]¶

Set the project ID

Parameters: name (str) – project_id

class pythologist_reader.formats.inform.sets.CellProjectInForm(h5path, mode='r')[source]¶

property gates¶: Get all the gates from the frames / samples in the project

qc(*args, **kwargs)[source]¶: Returns: QC: QC class to do quality checks

read_path(path, project_name=None, sample_name_index=None, channel_abbreviations=None, verbose=False, require=True, require_score=True, skip_segmentation_processing=False, microns_per_pixel=None, **kwargs)[source]¶

Read in the project folder

Parameters

path (str) – location of the project directory
project_name (str) – name of the project
sample_name_index (int) – where in the directory chain is the foldername that is the sample name if not set use full path. -1 is last directory
channel_abbreviations (dict) – dictionary of shortcuts to translate to simpler channel names
verbose (bool) – if true print extra details
require (bool) – if true (default), require that channel componenet image be present
require_score (bool) – if true (default), require there be a score file in the data
skip_segmentation_processing (bool) – if false (default), it will store the cellmap and edgemap images, if true, it will skip these steps to save time but downstream applications will not be able to generate the cell-cell contact measurements or segmentation images.
microns_per_pixel (float) – conversion factor

class pythologist_reader.formats.inform.custom.CellProjectInFormCustomMask(h5path, mode='r')[source]¶

Read in a project that has a region set by a custon hand drawn area

Accessed via read_path with the additonal parameters

read_path(*args, **kwargs)[source]¶

Read in the project folder

Parameters

path (str) – location of the project directory
project_name (str) – name of the project
sample_name_index (int) – where in the directory chain is the foldername that is the sample name if not set use full path. -1 is last directory
channel_abbreviations (dict) – dictionary of shortcuts to translate to simpler channel names
verbose (bool) – if true print extra details
require (bool) – if true (default), require that channel componenet image be present
skip_segmentation_processing (bool) – if false (default), it will store the cellmap and edgemap images, if true, it will skip these steps to save time but downstream applications will not be able to generate the cell-cell contact measurements or segmentation images.
microns_per_pixel (float) – conversion factor
custom_mask_name (str) – the mask name that will end in <maskname>.tif
other_mask_name (str) – what you want to call areas not contained in your custom mask

class pythologist_reader.formats.inform.custom.CellProjectInFormLineArea(h5path, mode='r')[source]¶

Read in a project that has a region set by a custon hand drawn area, and a margin set by a line

Accessed via read_path with the additonal parameters

read_path(*args, **kwargs)[source]¶

Read in the project folder

Parameters

path (str) – location of the project directory
project_name (str) – name of the project
sample_name_index (int) – where in the directory chain is the foldername that is the sample name if not set use full path. -1 is last directory
channel_abbreviations (dict) – dictionary of shortcuts to translate to simpler channel names
verbose (bool) – if true print extra details
require (bool) – if true (default), require that channel componenet image be present
require_score (bool) – if true (default), require that score be present
skip_segmentation_processing (bool) – if false (default), it will store the cellmap and edgemap images, if true, it will skip these steps to save time but downstream applications will not be able to generate the cell-cell contact measurements or segmentation images.
microns_per_pixel (float) – conversion factor
steps (int) – how many pixels out from the hand drawn line to consider the margin

class pythologist_reader.formats.inform.immunoprofile.CellProjectInFormImmunoProfile(*argv, **kwargs)[source]¶

Read an ImmunoProfile sample

add_sample_path(path, sample_name=None, export_names=['FOXP3', 'PD1_PDL1'], channel_abbreviations={'Foxp3 (Opal 570)': 'FOXP3', 'PD-1 (Opal 620)': 'PD1', 'PD-L1 (Opal 520)': 'PDL1'}, verbose=False, microns_per_pixel=0.496, invasive_margin_width_microns=40, invasive_margin_drawn_line_width_pixels=10, skip_margin=False, skip_segmentation_processing=False, skip_all_regions=False, deidentify=False, **kwargs)[source]¶

Read add a sample in as single project folder and add it to the CellProjectInFormImmunoProfile

such as IP-99-A00001:

IP-99-A00001/

└── INFORM_ANALYSIS

├── FOXP3
├── GIMP
└── PD1_PDL1

Parameters

path (str) – location of the project directory
sample_name (str) – name of the immunoprofile sample (default: rightmost directory in path), can be overridden by ‘deidenitfy’ set to True .. results in the uuid4 for the sample being used
export_names (list) – specify the names of the exports to read
channel_abbreviations (dict) – dictionary of shortcuts to translate to simpler channel names
verbose (bool) – if true print extra details
microns_per_pixel (float) – conversion factor
invasive_margin_width_microns (int) – size of invasive margin in microns
invasive_margin_drawn_line_width_pixels (int) – size of the line drawn for invasive margins in pixels
skip_margin (bool) – if false (default) read in margin line and define a margin acording to steps. if true, only read a tumor and stroma.
skip_segmentation_processing (bool) – if false (default) read segementations, else skip to run faster
deidentify (bool) – if false (default) use sample names and frame names derived from the folders. If true use the uuid4s.

Returns

sample_id, sample_name (tuple) returns the uuid4 assigned as the sample_id, and the sample_name that were given to this sample that was added

class pythologist_reader.formats.inform.immunoprofile.CellSampleInFormImmunoProfile[source]¶

read_path(path, sample_name=None, channel_abbreviations=None, verbose=False, require=True, require_score=True, steps=76, skip_margin=False, skip_segmentation_processing=False, skip_all_regions=False, export_names=[], deidentify=False)[source]¶

Read in the project folder

Parameters

path (str) – location of the project directory
project_name (str) – name of the project
sample_name_index (int) – where in the directory chain is the foldername that is the sample name if not set use full path. -1 is last directory
channel_abbreviations (dict) – dictionary of shortcuts to translate to simpler channel names
verbose (bool) – if true print extra details
require (bool) – if true (default), require that channel componenet image be present
require_score (bool) – if true (default), require that score file be present
skip_segmentation_processing (bool) – if false (default), it will store the cellmap and edgemap images, if true, it will skip these steps to save time but downstream applications will not be able to generate the cell-cell contact measurements or segmentation images.
microns_per_pixel (float) – conversion factor

class pythologist_reader.CellSampleGeneric[source]¶

property cdf¶: Return the pythologist.CellDataFrame of the sample

property frame_ids¶: Return the list of frame IDs

frame_iter()[source]¶

An iterator of frames

Returns: CellFrameGeneric

get_frame(frame_id)[source]¶

Parameters: frame_id (str) – the ID of the frame you want to access
Returns: the cell frame
Return type: CellFrameGeneric

property id¶: Return the UUID4 str

property key¶: Return a pandas.DataFrame of info about the sample

class pythologist_reader.CellFrameGeneric[source]¶

A generic CellFrameData object

binary_calls()[source]¶: Return all the binary feature calls (alias)

property cdf¶: Return the pythologist.CellDataFrame of the frame

cell_map()[source]¶: Return a dataframe of cell ID’s and locations

cell_map_image()[source]¶: Return a the image of cells by ID’s

edge_map()[source]¶: Return a dataframe of cells by ID’s of coordinates only on the edge of the cells

edge_map_image()[source]¶: Return an image of edges of integers by ID

get_channels(all=False)[source]¶

Return a dataframe of the Channels

Parameters: all (bool) – default False if all is set to true will also include excluded channels (like autofluoresence)
Returns: channel information
Return type: pandas.DataFrame

get_data(table_name)[source]¶

Get the data table

Parameters: table_name (pandas.DataFrame) – the table you access by name

get_image(image_id)[source]¶

Parameters: image_id (str) – get the image by this id
Returns: an image representing a 2d array
Return type: numpy.array

get_raw(feature_label, statistic_label, all=False, channel_abbreviation=True)[source]¶

Get the raw data

Parameters

feature_label (str) – name of the feature
statistic_label (str) – name of the statistic to extract
all (bool) – default False if True put out everything including excluded channels
channel_abbreviation (bool) – default True means use the abbreivations if available

Returns

the dataframe

Return type

pandas.DataFrame

property id¶: Returns the project UUID4

interaction_map()[source]¶

Returns: return a dataframe of which cells are in contact with one another
Return type: pandas.DataFrame

phenotype_calls()[source]¶: Return all the binary feature calls

property processed_image¶: Returns (numpy.array) of the processed_image

property processed_image_id¶: Returns (str) id of the frame object

segmentation_info()[source]¶: Return a dataframe with info about segmentation like cell areas and circumferences

set_data(table_name, table)[source]¶

Set the data table

Parameters

table_name (str) – the table name
table (pd.DataFrame) – the input table

set_interaction_map(touch_distance=1)[source]¶

Measure the cell-cell contact interactions

Parameters: touch_distance (int) – optional default is 1 distance to look away from a cell for another cell

set_processed_image_id(image_id)[source]¶

Parameters: image_id (str) – set the id of the frame object

set_regions(regions, use_processed_region=True, unset_label='undefined', verbose=False)[source]¶

Alter the regions in the frame

Parameters

regions (dict) – a dictionary of mutually exclusive region labels and binary masks if a region does not cover all the workable areas then it will be the only label and the unused area will get the ‘unset_label’ as a different region
use_processed_region (bool) – default True keep the processed region subtracted
unset_label (str) – name of unset regions default (undefined)

property shape¶: Returns the (tuple) shape of the image (rows,columns)

property table_names¶: Return a list of data table names

Welcome to pythologist-reader’s documentation!¶

Modules¶

Indices and tables¶