Kymo¶

lumicks.pylake.kymo.Kymo

class Kymo(name, file, start, stop, metadata, position_offset=0, calibration=None)¶

A Kymograph exported from Bluelake

Parameters

name (str) – Kymograph name
file (lumicks.pylake.File) – Parent file. Contains the channel data.
start (int) – Start point in the relevant info wave.
stop (int) – End point in the relevant info wave.
metadata (ScanMetaData) – Metadata for this Kymo.
position_offset (float) – Coordinate position offset with respect to the original raw data.
calibration (PositionCalibration) – Class defining calibration from microns to desired position units.

__getitem__(item)¶: All indexing is in timestamp units (ns)

calibrate_to_kbp(length_kbp)¶

Calibrate from microns to other units.

Parameters: length (float) – length of the kymo in kilobase pairs

crop_and_calibrate(channel='rgb', tether_length_kbp=None, **kwargs)¶

Open a widget to interactively edit the image stack.

Actions

left-click and drag to define the cropped ROI

Parameters

channel ('rgb', 'red', 'green', 'blue', None; optional) – Channel to plot for RGB images (None defaults to ‘rgb’) Not used for grayscale images
tether_length_kbp (float) – Length of the tether in the cropped region in kilobase pairs. If provided, the kymo returned from the image property will be automatically calibrated to this tether length.
**kwargs – Forwarded to Kymo.plot().

Examples

from lumicks import pylake
import matplotlib.pyplot as plt

# Loading a stack.
h5_file = pylake.File("example.h5")
_, kymo = h5_file.kymos.popitem()
widget = kymo.crop_and_calibrate("green", 48.502)
plt.show()

# Select cropping ROI by left-click drag

# Grab the updated image stack
new_kymo = widget.kymo

crop_by_distance(lower, upper)¶

Crop the kymo by position.

Crops the kymograph down to lower <= x < upper.

Parameters

lower (float) – Lower bound in physical units.
upper (float) – Upper bound in physical units.

downsampled_by(time_factor=1, position_factor=1, reduce=<function sum>)¶

Return a copy of this Kymograph which is downsampled by time_factor in time and position_factor in space.

Parameters

time_factor (int) – The number of pixels that will be averaged in time (default: 1).
position_factor (int) – The number of pixels that will be averaged in space (default: 1).
reduce (callable) – The numpy function which is going to reduce multiple pixels into one. The default is np.sum.

export_tiff(filename, *, dtype=<class 'numpy.float32'>, clip=False)¶

Save the RGB photon counts to a TIFF image

Parameters

filename (str) – The name of the TIFF file where the image will be saved.
dtype (np.dtype) – The data type of a single color channel in the resulting image.
clip (bool) – If enabled, the photon count data will be clipped to fit into the desired dtype. This option is disabled by default: an error will be raise if the data does not fit.

flip()¶: Flip the kymograph along the positional axis

classmethod from_dataset(h5py_dset, file)¶

Construct a confocal class from dataset.

Parameters

h5py_dset (h5py.Dataset) – The original HDF5 dataset containing confocal scan information
file (lumicks.pylake.File) – The parent file. Used to loop up channel data

get_image(channel='rgb') → numpy.ndarray¶

Get image data for the full stack as an ndarray.

Parameters: channel ({'red', 'green', 'blue', 'rgb'}) – The color channel of the requested data.

line_timestamp_ranges(exclude=None, *, include_dead_time=None)¶

Get start and stop timestamp of each line in the kymo.

Note: The stop timestamp for each line is defined as the first sample past the end of the relevant data such that the timestamps can be used for slicing directly.

Parameters

exclude (bool) – Exclude dead time at the end of each frame (deprecated)
include_dead_time (bool) – Include dead time at the end of each frame (default: False).

plot(channel='rgb', *, adjustment=<lumicks.pylake.adjustments.ColorAdjustment object>, axes=None, image_handle=None, show_title=True, **kwargs)¶

Plot a kymo for the requested color channel(s).

Parameters

channel ({"red", "green", "blue", "rgb"}, optional) – Color channel to plot.
adjustment (lk.ColorAdjustment) – Color adjustments to apply to the output image.
axes (matplotlib.axes.Axes, optional) – If supplied, the axes instance in which to plot.
image_handle (matplotlib.image.AxesImage or None) – Optional image handle which is used to update plots with new data rather than reconstruct them (better for performance).
show_title (bool, optional) – Controls display of auto-generated plot title
**kwargs – Forwarded to matplotlib.pyplot.imshow(). These arguments are ignored if image_handle is provided.

Returns

The image handle representing the plotted image.

Return type

matplotlib.image.AxesImage

plot_blue(**kwargs)¶: Plot an image of the blue photon channel

Deprecated since version 0.11.1: This method will be removed in a future release. Use plot(channel='blue') instead.

plot_green(**kwargs)¶: Plot an image of the green photon channel

Deprecated since version 0.11.1: This method will be removed in a future release. Use plot(channel='green') instead.

plot_red(**kwargs)¶: Plot an image of the red photon channel

Deprecated since version 0.11.1: This method will be removed in a future release. Use plot(channel='red') instead.

plot_rgb(**kwargs)¶: Plot an image of all color channels.

Deprecated since version 0.11.1: This method will be removed in a future release. Use plot(channel='rgb') instead.

plot_with_force(force_channel, color_channel, aspect_ratio=0.25, reduce=<function mean>, kymo_args={}, adjustment=<lumicks.pylake.adjustments.ColorAdjustment object>, **kwargs)¶

Plot kymo with force channel downsampled over scan lines

Note that high frequency channel data must be available for this function to work.

Parameters

force_channel (str) – name of force channel to downsample and plot (e.g. ‘1x’)
color_channel (str) – color channel of kymo to plot (‘red’, ‘green’, ‘blue’, ‘rgb’)
aspect_ratio (float) – aspect ratio of the axes (i.e. ratio of y-unit to x-unit)
reduce (callable) – The numpy function which is going to reduce multiple samples into one. Forwarded to Slice.downsampled_over()
kymo_args (dict) – Forwarded to matplotlib.pyplot.imshow()
adjustment (lk.ColorAdjustment) – Color adjustments to apply to the output image.
**kwargs – Forwarded to Slice.plot().

plot_with_position_histogram(color_channel, pixels_per_bin=1, hist_ratio=0.25, adjustment=<lumicks.pylake.adjustments.ColorAdjustment object>, **kwargs)¶

Plot kymo with histogram along position axis

Parameters

color_channel (str) – color channel of kymo to plot (‘red’, ‘green’, ‘blue’, ‘rgb’).
pixels_per_bin (int) – number of pixels along position axis to bin together.
hist_ratio (float) – width of the histogram with respect to the kymo image.
adjustment (lk.ColorAdjustment) – Color adjustments to apply to the output image.
**kwargs – Forwarded to histogram bar plot.

plot_with_time_histogram(color_channel, pixels_per_bin=1, hist_ratio=0.25, adjustment=<lumicks.pylake.adjustments.ColorAdjustment object>, **kwargs)¶

Plot kymo with histogram along time axis

Parameters

color_channel (str) – color channel of kymo to plot (‘red’, ‘green’, ‘blue’, ‘rgb’).
pixels_per_bin (int) – number of pixels along time axis to bin together.
hist_ratio (float) – height of the histogram with respect to the kymo image.
adjustment (lk.ColorAdjustment) – Color adjustments to apply to the output image.
**kwargs – Forwarded to histogram bar plot.

save_tiff(filename, dtype=<class 'numpy.float32'>, clip=False)¶: Deprecated since version 0.13.0: This method has been renamed to export_tiff() to more accurately reflect that it is exporting to a different format.

property blue_image¶: Returns an image representing the blue channel

Deprecated since version 0.12.0: This property will be removed in a future release. Use get_image('blue') instead.

property center_point_um¶: Returns a dictionary of the x/y/z center coordinates of the scan (w.r.t. brightfield field of view)

property contiguous¶

Are the pixels integrated over a contiguous period of time

If this flag is false then pixels have been integrated over disjoint sections of time. This can be the case when a kymograph has been downsampled over time.

property duration¶: Duration of the kymograph in seconds. This value is equivalent to the number of scan lines times the line time in seconds. It does not take into account incomplete scan lines or mirror fly-in/out time.

property fast_axis¶: The axis that was scanned (x or y)

property green_image¶: Returns an image representing the green channel

Deprecated since version 0.12.0: This property will be removed in a future release. Use get_image('green') instead.

property line_time_seconds¶: Line time in seconds

property pixel_time_seconds¶: Pixel dwell time in seconds

property pixels_per_line¶: Number of pixels in each line

property pixelsize¶: Returns a List of axes dimensions in calibrated units. The length of the list corresponds to the number of scan axes.

property pixelsize_um¶: Returns a List of axes dimensions in um. The length of the list corresponds to the number of scan axes.

property red_image¶: Returns an image representing the red channel

Deprecated since version 0.12.0: This property will be removed in a future release. Use get_image('red') instead.

property rgb_image¶: Returns an rgb image

Deprecated since version 0.12.0: This property will be removed in a future release. Use get_image('rgb') instead.

property shape¶: Shape of the reconstructed Kymo image

property size_um¶: Returns a List of scan sizes in um along axes. The length of the list corresponds to the number of scan axes.

property timestamps: numpy.ndarray¶

Timestamps for each image pixel.

The returned array has the same shape as the color_image arrays. Timestamps are defined at the mean of the timestamps.