lumicks.pylake.kymo.Kymo¶

class Kymo(name, file, start, stop, json, 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.
json : dict: Dictionary containing kymograph-specific metadata.
position_offset : float: Coordinate position offset with respect to the original raw data.
calibration : PositionCalibration: Class defining calibration from microns to desired position units.

__init__(name, file, start, stop, json, position_offset=0, calibration=None)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(name, file, start, stop, json[, …])	Initialize self.
`calibrate_to_kbp`(length_kbp)	Calibrate from microns to other units.
`crop_by_distance`(lower, upper)	Crop the kymo by position.
`downsampled_by`([time_factor, …])	Return a copy of this Kymograph which is downsampled by `time_factor` in time and `position_factor` in space.
`from_dataset`(h5py_dset, file)	Construct a confocal class from dataset.
`plot_blue`(**kwargs)	Plot an image of the blue photon channel
`plot_green`(**kwargs)	Plot an image of the green photon channel
`plot_red`(**kwargs)	Plot an image of the red photon channel
`plot_rgb`(**kwargs)	Plot a full rbg kymograph image
`plot_with_force`(force_channel, color_channel)	Plot kymo with force channel downsampled over scan lines
`plot_with_position_histogram`(color_channel)	Plot kymo with histogram along position axis
`plot_with_time_histogram`(color_channel[, …])	Plot kymo with histogram along time axis
`save_tiff`(filename[, dtype, clip])	Save the RGB photon counts to a TIFF image

Attributes

`blue_image`
`blue_photon_count`
`blue_power`
`center_point_um`	Returns a dictionary of the x/y/z center coordinates of the scan (w.r.t.
`fast_axis`
`green_image`
`green_photon_count`
`green_power`
`has_fluorescence`	Deprecated since version 0.8.0.
`has_force`	Deprecated since version 0.8.0.
`infowave`
`json`	Deprecated since version 0.8.0.
`line_time_seconds`	Line time in seconds
`pixels_per_line`
`pixelsize`	Returns a `List` of axes dimensions in calibrated units.
`pixelsize_um`	Returns a `List` of axes dimensions in um.
`red_image`
`red_photon_count`
`red_power`
`rgb_image`
`scan_width_um`	Returns a `List` of scan widths as configured in the Bluelake UI. The length of the list
`size_um`	Returns a `List` of scan sizes in um along axes.
`sted_power`
`timestamps`	Timestamps for image pixels, not for samples

__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_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`.

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

plot_blue(**kwargs)¶

Plot an image of the blue photon channel

Parameters:	**kwargs Forwarded to `matplotlib.pyplot.imshow()`.

plot_green(**kwargs)¶

Plot an image of the green photon channel

Parameters:	**kwargs Forwarded to `matplotlib.pyplot.imshow()`.

plot_red(**kwargs)¶

Plot an image of the red photon channel

Parameters:	**kwargs Forwarded to `matplotlib.pyplot.imshow()`.

plot_rgb(**kwargs)¶

Plot a full rbg kymograph image

Parameters:	**kwargs Forwarded to `matplotlib.pyplot.imshow()`.

plot_with_force(force_channel, color_channel, aspect_ratio=0.25, reduce=<function mean>, **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()
**kwargs: Forwarded to Slice.plot().

plot_with_position_histogram(color_channel, pixels_per_bin=1, hist_ratio=0.25, **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. **kwargs Forwarded to histogram bar plot.

plot_with_time_histogram(color_channel, pixels_per_bin=1, hist_ratio=0.25, **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. **kwargs Forwarded to histogram bar plot.

save_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.

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

has_fluorescence¶: Deprecated since version 0.8.0: By definition, confocal images always have fluorescence data.

has_force¶: Deprecated since version 0.8.0: This property is always False and therefore not needed.

json¶: Deprecated since version 0.8.0: Access to raw metadata will be removed in a future release. Use accessor properties instead. (see docs)

line_time_seconds¶: Line time in seconds

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

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

scan_width_um¶

Returns a List of scan widths as configured in the Bluelake UI. The length of the list: corresponds to the number of scan axes. Note that these widths can deviate from the actual scan widths performed in practice

Deprecated since version 0.8.2: The property scan_width_um has been deprecated. Use size_um to get the actual size of the scan. When performing a scan, Bluelake determines an appropriate scan width based on the desired pixel size and the desired scan width. This means that the size of the performed scan could deviate from the width provided in this 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.

timestamps¶

Timestamps for image pixels, not for samples

The returned array has the same shape as the *_image arrays.