lumicks.pylake.kymo.Kymo¶

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

A Kymograph exported from Bluelake

Parameters

namestr: Kymograph name
filelumicks.pylake.File: Parent file. Contains the channel data.
startint: Start point in the relevant info wave.
stopint: End point in the relevant info wave.
jsondict: Dictionary containing kymograph-specific metadata.
position_offsetfloat: Coordinate position offset with respect to the original raw data.
calibrationPositionCalibration: Class defining calibration from microns to desired position units.

__init__(name, file, start, stop, json, position_offset=0, calibration=None)¶

Methods

`__getitem__`(item)	All indexing is in timestamp units (ns)
`_downsample_channel`(channel[, reduce])
`_fix_incorrect_start`()	Resolve error when confocal scan starts before the timeline information.
`_get_laser_power`(name)
`_get_photon_count`(name)	Grab the portion of the photon count that overlaps with the scan.
`_get_plot_data`(channel[, adjustment, frame])	Get image data for plotting requested channel.
`_has_default_factories`()
`_image`(channel)
`_line_start_timestamps`()	Compute starting timestamp of each line (first DAQ sample corresponding to that line), not the first pixel timestamp.
`_ordered_axes`()	Returns axis indices in spatial order
`_plot`(channel, axes[, adjustment])	Plot a kymo for requested color channel(s).
`_timestamps`(channel[, reduce])
`_to_spatial`(data)	Spatial data as rows, time as columns
`calibrate_to_kbp`(length_kbp)	Calibrate from microns to other units.
`crop_and_calibrate`([channel, tether_length_kbp])	Open a widget to interactively edit the image stack.
`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.
`get_image`([channel])	Get image data for the full stack as an `np.ndarray`.
`plot`(channel[, axes])	Show a formatted plot for the requested color channel.
`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 an image of all color channels.
`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

`_num_pixels`
`_scan_order`	Order in which the axes are scanned.
`_shape`	The shape of the image ([optional: pixels on slow axis], pixels on fast axis)
`blue_image`	Deprecated since version 0.12.0.
`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`	Deprecated since version 0.12.0.
`green_photon_count`
`green_power`
`infowave`
`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`	Deprecated since version 0.12.0.
`red_photon_count`
`red_power`
`rgb_image`	Deprecated since version 0.12.0.
`size_um`	Returns a `List` of scan sizes in um along axes.
`sted_power`
`timestamps`	Timestamps for image pixels, not for samples