PointScan

lumicks.pylake.point_scan.PointScan

class PointScan(name, file, start, stop, metadata)

A confocal point scan exported from Bluelake

Parameters

  • name (str) – point scan 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 scan-specific metadata.

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(channel='rgb', *, axes=None, show_title=True, **kwargs)

Plot photon counts for the selected channel(s).

Parameters

  • channel ({"red", "green", "blue", "rgb"}, optional) – Color channel to plot.

  • axes (matplotlib.axes.Axes, optional) – If supplied, the axes instance in which to plot.

  • show_title (bool, optional) – Controls display of auto-generated plot title

  • **kwargs – Forwarded to matplotlib.pyplot.plot()

Returns

A list of lines representing the plotted data.

Return type

List[matplotlib.lines.Line2D]

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.

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 pixel_time_seconds

Pixel dwell time in seconds