molyso.mm package¶
MM Module, contains Mother Machine analysis specific functionality.
molyso.mm.cell_detection module¶
documentation
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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
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bottom
¶ Returns the absolute (on rotated image) coordinate of the cell bottom.
Returns:
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cell_image
¶ The cell image, cropped out of the channel image.
Returns: image Return type: numpy.ndarray
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centroid
¶ Returns the (absolute coordinate on rotated image) centroid (2D). :return: :rtype: list
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centroid_1d
¶ Returns the (one dimensional) (absolute coordinate on rotated image) centroid. :return: centroid :rtype: float
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channel
¶
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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
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length
¶ Returns the cell length.
Returns: length
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local_bottom
¶
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local_top
¶
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top
¶ Returns the absolute (on rotated image) coordinate of the cell top.
Returns: top
molyso.mm.channel_detection module¶
documentation
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class
molyso.mm.channel_detection.
Channel
(image, left, right, top, bottom)[source]¶ Bases:
object
Parameters: - image –
- left –
- right –
- top –
- bottom –
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bottom
¶ Returns:
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cells
¶
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cells_type
¶ alias of
molyso.mm.cell_detection.Cells
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centroid
¶ Returns:
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channel_image
¶
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image
¶
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left
¶
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putative_orientation
¶
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real_bottom
¶
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real_top
¶
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right
¶
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top
¶ Returns:
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class
molyso.mm.channel_detection.
Channels
(image, bootstrap=True)[source]¶ Bases:
object
docstring
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centroids
¶ Returns:
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channels_list
¶
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image
¶
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nearest_tree
¶
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molyso.mm.fluorescence module¶
molyso.mm.highlevel module¶
molyso.mm.highlevel_interactive_ground_truth module¶
documentation
molyso.mm.highlevel_interactive_viewer module¶
documentation
molyso.mm.image module¶
molyso.mm.tracking module¶
documentation
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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.
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align_channels
(progress_indicator=<callable_iterator object>)[source]¶ Parameters: progress_indicator –
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guess_channel_orientation
()[source]¶ Tries to guess the channel orientation. 1 if the closed end (‘mother side’) is the high coordinates, -1 if low …
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logger
¶
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molyso.mm.tracking.
analyse_cell_fates
(tracker, previous_cells, current_cells)[source]¶ Parameters: - tracker –
- previous_cells –
- current_cells –
Returns:
molyso.mm.tracking_infrastructure module¶
This module contains cell tracking infrastructure.
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class
molyso.mm.tracking_infrastructure.
CellCrossingCheckingGlobalDuoOptimizerQueue
[source]¶ Bases:
object
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class
molyso.mm.tracking_infrastructure.
CellTracker
[source]¶ Bases:
object
The CellTracker contains all tracks of a channel.
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all_tracked_cells
¶
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average_cells
¶ Returns the average count of cells present in this tracked channel.
Returns:
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get_cell_by_observation
(where)[source]¶ Returns the associated cell by its observation.
Parameters: where – Returns:
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new_observed_cell
(where)[source]¶ Creates a new TrackedCell object, with added observation.
Parameters: where – Returns:
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new_observed_origin
(where)[source]¶ Creates a new TrackedCell object and adds it as an origin, with added observation. :param where: :return:
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origins
¶
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timepoints
¶
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molyso.mm.tracking_output module¶
documentation
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molyso.mm.tracking_output.
analyze_tracking
(cells, receptor, meta=None)[source]¶ Parameters: - meta –
- cells –
- receptor –
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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
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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
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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 –
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molyso.mm.tracking_output.
s_to_h
(s)[source]¶ converts seconds to hours :param s: seconds :return: hours