Getting photon counts

[spangeni]

Is there a way to get blue and red photon counts after tracking the kymolines.For example, if i use tracegreedy then have 4 kymo lines, i wanted to know if i can extract photon counts for each of the kymolines apart from position and coordinates.To be specific, I wanted to have a way to get the photon counts of specific kymolines from kymograph that has many kymolines.Any suggestions would be helpful.

[JoepVanlier]

Hi,

sorry, I didn't see your question until today.

You can sample the photon counts by iterating over the Kymoline lists. See the following for an example: https://lumicks-pylake.readthedocs.io/en/latest/tutorial/kymotracking.html#extracting-summed-intensities

For a single trace, it looks something like this:

longest_trace.sample_from_image(num_pixels=5)

This will sum the counts for each point on that trace in 5 pixels in either direction (from position - num_pixels to (and including) position + num_pixels).

If you want to do this for all your kymolines, you can iterate over them.

sampled_counts = []
for line in kymowidget.lines:
    sampled_counts.append(line.sample_from_image(num_pixels=5))

print(sampled_counts)

We can also write that a bit shorter using a list comprehension:

sampled_counts = [line.sample_from_image(num_pixels=5) for line in kymowidget.lines]

I hope I'm interpreting your question correctly. If the question is more related to identifying which Kymoline is which then I'm afraid we don't have specific functionality for that yet. What you could do is select your line of interest by dragging a region to track using the right mouse button, rather than using track all button.

Maybe you can explain a little more about your use case. What are you trying to achieve?