scripts.GUIhelpers#

Classes#

`AxisSelector`
`GatingCheckBox`
`GatingMixin`	A mixin that provides gating-related UI functionality.
`GuiMessages`
`LabeledComboBox`
`LabeledSpinBox`
`LiveDeadDebrisSelectors`	Mixin class to display the 2 basic stains for live/dead and cells/debris entries.
`StainSelector`

Functions#

iterate_stains(self)

Return a dictionary with the extra stains settings as provided by the user in CS GUI

load_fcs_file(fcss)

param fcss:: List of fcs files provided by the user

Module Contents#

class scripts.GUIhelpers.AxisSelector(label_text, parent=None)#

Bases: PyQt5.QtWidgets.QWidget

set_items(items)#

combo#

label#

class scripts.GUIhelpers.GatingCheckBox#

gating_checkbox()#

class scripts.GUIhelpers.GatingMixin#

A mixin that provides gating-related UI functionality. A thread on mixin: https://stackoverflow.com/questions/533631/what-is-a-mixin-and-why-is-it-useful

This mixin defines the `toggle_gating_options` method, which shows or hides UI elements related to gating based on the state of a checkbox.

get_host_class_name()#

toggle_gating_options()#

class scripts.GUIhelpers.GuiMessages#

AXIS_SELECTION = 'Choose the Channels that will be used as x, y, z axis for the 3D plot:'#

BLANKS_MULTIFILES = 'If you wish to use several files, please add them all at once.Every time you click on the...#

COLUMN_NAMES_ERROR = 'Column names on your coculture files differ. Please make sure you only include files sharing...#

GATING_CHECHBOX = 'When staining for both inactive and total cells, CellScanner will also returnthe living cells,...#

GATING_THRESHOLD = 'Important: Some visualization software may transform raw data.Ensure you set the threshold...#

PREVIOUSLY_TRAINED_MODEL = 'Optional. If you have a model from a previous CellScanner run,you may provide it so you do not...#

UNCERTAINTY_CHECKBOX = 'Apply filtering on the predictions based on their uncertainty scores.'#

UNCERTAINTY_TOOLTIP = 'Set threshold for filtering out uncertain predictions. If you just trained a model, CellScanner...#

USER_STAIN_TOOLTIP = 'Select the channel that will be used for gating cells. All events where the threshold is met...#

class scripts.GUIhelpers.LabeledComboBox(label_text, items=None, default=None, parent=None)#

Bases: PyQt5.QtWidgets.QWidget

combo#

label#

class scripts.GUIhelpers.LabeledSpinBox(label_text, min_value=0, max_value=1000, step=1, default_value=0, parent=None)#

Bases: PyQt5.QtWidgets.QWidget

label#

spin_box#

class scripts.GUIhelpers.LiveDeadDebrisSelectors#

Mixin class to display the 2 basic stains for live/dead and cells/debris entries.

basic_stains()#

class scripts.GUIhelpers.StainSelector(label_text, tooltip_text, parent=None)#

Bases: PyQt5.QtWidgets.QWidget

set_items(items)#

combo#

label#

relation#

threshold#

scripts.GUIhelpers.iterate_stains(self)#: Return a dictionary with the extra stains settings as provided by the user in CS GUI

scripts.GUIhelpers.load_fcs_file(fcss)#

Parameters:: fcss – List of fcs files provided by the user
Return sample_to_df:
Return sample_numeric_columns: