molyso.mm package¶

MM Module, contains Mother Machine analysis specific functionality.

molyso.mm.cell_detection module¶

documentation

class molyso.mm.cell_detection.Cell(top, bottom, channel)[source]¶

Bases: object

A Cell.

Parameters:	top – coordinate of the ‘top’ of the cell, in channel coordinates bottom – coordinate of the ‘bottom’ of the cell, in channel coordinates channel – Channel object the cell belongs to

bottom¶

Returns the absolute (on rotated image) coordinate of the cell bottom.

Returns:

cell_image¶

The cell image, cropped out of the channel image.

Returns:	image
Return type:	numpy.ndarray

centroid¶: Returns the (absolute coordinate on rotated image) centroid (2D). :return: :rtype: list

centroid_1d¶: Returns the (one dimensional) (absolute coordinate on rotated image) centroid. :return: centroid :rtype: float

channel¶

crop_out_of_channel_image(channel_image)[source]¶

Crops the clel out of a provided image. Used internally for Cell.cell_image(), and to crop cells out of fluorescence channel images.

Parameters:	channel_image (numpy.ndarray) –
Returns:	image
Return type:	numpy.ndarray

length¶

Returns the cell length.

Returns:	length

local_bottom¶

local_top¶

top¶

Returns the absolute (on rotated image) coordinate of the cell top.

Returns:	top

class molyso.mm.cell_detection.Cells(channel, bootstrap=True)[source]¶

Bases: object

A Cells object, a collection of Cell objects.

cell_type¶: alias of Cell

cells_list¶

centroids¶

Returns the centroids of the cells.

Returns:	centroids
Return type:	list

channel¶

clean()[source]¶: Performs clean-up.

nearest_tree¶

molyso.mm.cell_detection.find_cells_in_channel(image)[source]¶

molyso.mm.cell_detection.find_cells_in_channel_classic(image)[source]¶

Parameters:	image –
Returns:

molyso.mm.channel_detection module¶

documentation

class molyso.mm.channel_detection.Channel(image, left, right, top, bottom)[source]¶

Bases: object

Parameters:	image – left – right – top – bottom –

bottom¶

Returns:

cells¶

cells_type¶: alias of molyso.mm.cell_detection.Cells

centroid¶

Returns:

channel_image¶

clean()[source]¶: Peforms clean up routines.

crop_out_of_image(image)[source]¶

Parameters:	image –
Returns:

detect_cells()[source]¶: Performs Cell detection (by instantiating a Cells object).

get_coordinates()[source]¶

Returns:

image¶

left¶

putative_orientation¶

real_bottom¶

real_top¶

right¶

top¶

Returns:

class molyso.mm.channel_detection.Channels(image, bootstrap=True)[source]¶

Bases: object

docstring

align_with_and_return_indices(other_channels)[source]¶

Parameters:	other_channels –
Returns:

centroids¶

Returns:

channel_type¶: alias of Channel

channels_list¶

clean()[source]¶: Performs clean up routines.

find_nearest(pos)[source]¶

Parameters:	pos –
Returns:

image¶

nearest_tree¶

molyso.mm.channel_detection.alternate_vertical_channel_region_detection(image)[source]¶

Parameters:	image –
Returns:

molyso.mm.channel_detection.find_channels(image)[source]¶: channel finder :param image: :return:

molyso.mm.channel_detection.horizontal_channel_detection(image)[source]¶: @param image: @return:

molyso.mm.channel_detection.vertical_channel_region_detection(image)[source]¶

Parameters:	image –
Returns:

molyso.mm.fluorescence module¶

molyso.mm.highlevel module¶

molyso.mm.highlevel_interactive_ground_truth module¶

documentation

molyso.mm.highlevel_interactive_ground_truth.interactive_ground_truth_main(args, tracked_results)[source]¶

Ground truth mode entry function.

Parameters:

args –
tracked_results –

Returns:

raise SystemExit:

molyso.mm.highlevel_interactive_viewer module¶

documentation

molyso.mm.highlevel_interactive_viewer.interactive_main(args)[source]¶

Parameters:	args –
Raises:	SystemExit –

molyso.mm.image module¶

molyso.mm.tracking module¶

documentation

class molyso.mm.tracking.TrackedPosition[source]¶

Bases: object

A TrackedPosition object contains various CellTracker objects for each channel within a multipoint position, as well as other information associated with the position.

align_channels(progress_indicator=<callable_iterator object>)[source]¶

Parameters:	progress_indicator –

find_first_valid_time()[source]¶: Finds the first valid time point for the position.

get_tracking_work_size()[source]¶

Returns:

guess_channel_orientation()[source]¶: Tries to guess the channel orientation. 1 if the closed end (‘mother side’) is the high coordinates, -1 if low …

logger¶

perform_everything(times)[source]¶

Parameters:	times –
Returns:

perform_tracking(progress_indicator=<callable_iterator object>)[source]¶

Parameters:	progress_indicator –

remove_empty_channels()[source]¶: Removes empty channels from the data set.

remove_empty_channels_post_tracking()[source]¶: Removes empty channels after tracking.

set_times(times)[source]¶

Parameters:	times –

molyso.mm.tracking.analyse_cell_fates(tracker, previous_cells, current_cells)[source]¶

Parameters:	tracker – previous_cells – current_cells –
Returns:

molyso.mm.tracking.each_k_tracking_tracker_channels_in_results(tracking)[source]¶

Parameters:	tracking –

molyso.mm.tracking.each_pos_k_tracking_tracker_channels_in_results(inner_tracked_results)[source]¶

Parameters:	inner_tracked_results –

molyso.mm.tracking_infrastructure module¶

This module contains cell tracking infrastructure.

class molyso.mm.tracking_infrastructure.CellCrossingCheckingGlobalDuoOptimizerQueue[source]¶

Bases: object

add_outcome(cost, involved_a, involved_b, what)[source]¶

Parameters:	cost – involved_a – involved_b – what –
Returns:

perform_optimal()[source]¶

Returns:

class molyso.mm.tracking_infrastructure.CellTracker[source]¶

Bases: object

The CellTracker contains all tracks of a channel.

all_tracked_cells¶

average_cells¶

Returns the average count of cells present in this tracked channel.

Returns:

get_cell_by_observation(where)[source]¶

Returns the associated cell by its observation.

Parameters:	where –
Returns:

is_tracked(cell)[source]¶

Returns whether the cell is tracked.

Parameters:	cell –
Returns:

new_cell()[source]¶

Creates a new TrackedCell object associated with this tracker.

Returns:

new_observed_cell(where)[source]¶

Creates a new TrackedCell object, with added observation.

Parameters:	where –
Returns:

new_observed_origin(where)[source]¶: Creates a new TrackedCell object and adds it as an origin, with added observation. :param where: :return:

new_origin()[source]¶

Creates a new TrackedCell object and adds it as an origin.

Returns:

origins¶

tick()[source]¶: Ticks the clock. Sets the internal timepoint counter forward by one.

timepoints¶

class molyso.mm.tracking_infrastructure.TrackedCell(tracker)[source]¶

Bases: object

Parameters:	tracker –

add_child(tcell)[source]¶

Parameters:	tcell –
Returns:

add_children(*children)[source]¶

Parameters:	children –

add_observation(cell)[source]¶

Parameters:	cell –
Returns:

children¶

elongation_rates¶

Returns:

parent¶

raw_elongation_rates¶

raw_trajectories¶

seen_as¶

tracker¶

trajectories¶

Returns:

ultimate_parent¶

Returns:

molyso.mm.tracking_infrastructure.to_list(x)[source]¶

Parameters:	x –
Returns:

molyso.mm.tracking_output module¶

documentation

molyso.mm.tracking_output.analyze_tracking(cells, receptor, meta=None)[source]¶

Parameters:	meta – cells – receptor –

molyso.mm.tracking_output.catch_attribute_error(what, otherwise)[source]¶: runs callable ‘what’ and catches AttributeError, returning ‘otherwise’ if one occurred :param what: callable :param otherwise: alternate result in case of IndexError :return: result of ‘what’ or ‘otherwise’ in case of IndexError

molyso.mm.tracking_output.catch_index_error(what, otherwise)[source]¶: runs callable ‘what’ and catches IndexErrors, returning ‘otherwise’ if one occurred :param what: callable :param otherwise: alternate result in case of IndexError :return: result of ‘what’ or ‘otherwise’ in case of IndexError

molyso.mm.tracking_output.get_object_unique_id(obj)[source]¶

Parameters:	obj –
Returns:

molyso.mm.tracking_output.iterate_over_cells(cells)[source]¶

Parameters:	cells –
Returns:

molyso.mm.tracking_output.plot_timeline(p, channels, cells, figure_presetup=None, figure_finished=None, show_images=True, show_overlay=True, leave_open=False)[source]¶

Parameters:	p – channels – cells – figure_presetup – figure_finished – show_images – show_overlay – leave_open –

molyso.mm.tracking_output.s_to_h(s)[source]¶: converts seconds to hours :param s: seconds :return: hours

molyso.mm.tracking_output.s_to_h_str(s, *args, **kwargs)[source]¶: converts seconds to hours as a rounded string :param s: seconds :return: hours :param s: seconds :return: hours string

molyso.mm.tracking_output.tracker_to_cell_list(tracker)[source]¶

Parameters:	tracker –
Returns: