4. Kymographs

Download this page as a Jupyter notebook

To load an HDF5 file and lists all of the kymographs inside of it, run:

import lumicks.pylake as lk

file = lk.File("example.h5")
list(file.kymos)  # e.g. shows: "['reference', 'sytox']"

Once again, .kymos is a regular Python dictionary so we can easily iterate over it:

# Plot all kymos in a file
for name, kymo in file.kymos.items():
    kymo.plot_rgb()
    plt.savefig(name)

Or just pick a single one:

kymo = file.kymos["name"]
kymo.plot_red()

4.1. Kymo data and details

Access the raw image data:

rgb = kymo.rgb_image  # matrix with `shape == (h, w, 3)`
blue = kymo.blue_image  # single color so `shape == (h, w)`

# Plot manually
plt.imshow(rgb)

Kymographs can also be sliced in order to obtain a specific time range. For example, one can plot the region of the kymograph between 175 and 180 seconds using:

kymo["175s":"180s"].plot_red()

There are also several properties available for convenient access to the kymograph metadata:

  • kymo.center_point_um provides a dictionary of the central x, y, and z coordinates of the scan in micrometers relative to the brightfield field of view
  • kymo.size_um provides a list of scan sizes in micrometers along the axes of the scan
  • kymo.pixelsize_um provides the pixel size in micrometers
  • kymo.pixels_per_line provides the number of pixels in each line of the kymograph
  • kymo.fast_axis provides the axis that was scanned (x or y)
  • kymo.line_time_seconds provides the time between successive lines

4.2. Plotting and exporting

There are also convenience functions to plot individual color channels and the full RGB image:

plt.subplot(2, 1, 1)
kymo.plot_rgb()
plt.subplot(2, 1, 2)
kymo.plot_blue()

The images can also be exported in the TIFF format:

kymo.save_tiff("image.tiff")