Contents

• setup_samples

setup_samples

This module consists of methods which configure ref:samples objects based on reference files.

microscope_automation.samples.setup_samples.get_colony_data(prefs, colony_file)

Get data and positions of colonies.

Input:

prefs: preferences with information about colony file

colony_file: path to .csv file with colony data.

Output:

colonies: pandas frame with content of .csv file

microscope_automation.samples.setup_samples.filter_colonies(prefs, colonies, well_dict)

Select colonies to image based on settings in preferences file.

Input:

prefs: preferences with selection criteria

colonies: table with colony data

well_dict: list with wells that should be considered. Well names in format ‘A1’.

Output:

slected_colonies: subset of colonies to be imaged

microscope_automation.samples.setup_samples.add_colonies(well_object, colonies, hardware_settings)

Add colonies from Celigo scan to well.

Input:

well_object: instance of well_object from module samples

colonies: pandas frame with colony information. This information was extracted with CellProfiler from plate-scanner images.

hardware_settings: preferences with description of microscope components, here coordinate transformation between colonies and well

Output:

colony_list: list with all colony objects

microscope_automation.samples.setup_samples.add_barcode(name, well_object, layout)

Add barcode to well.

Input:

name: string with name for barcode

well_object: instance of Well class from module samples

layout: preferences for plate layout

Output:

none

microscope_automation.samples.setup_samples.setup_plate(prefs, colony_file=None, microscope_object=None, barcode=None)

Create object of class plateholder from module sample that holds information about all colonies scanned with plate reader.

Input:

prefs: preferences file for experiment

colony_file: path to .csv file with colony data.

microscope_object: object create by setup_microscope describing hardware components

barcode: string barcode for plate. If not provided can be read from colony file or will be requested by pop-up window.

Output:

plate_holder_object: object that contains all wells with sample information.

microscope_automation.samples.setup_samples.setup_slide(prefs, microscope_object=None)

Create basic object of class slide from module sample that consists of plate holder and slide.

Input:

prefs: preferences file for experiment

Output:

plate_holder_object: object that contains one slide.