kymograph tutorial: add section on photon counts

docs/tutorial/kymographs.rst

@@ -140,6 +140,45 @@ This returns a new (but flipped) :class:`~lumicks.pylake.kymo.Kymo`::
 
 .. image:: figures/kymographs/kymo_flipped.png
 
+Extracting photon counts
+------------------------
+Photon counts can be extracted from the raw image, for example for stoichiometry analysis.
+First, select a region for which the photon counts have to be determined::
+
+    kymo_selection = kymo["88.5s":"93s"].crop_by_distance(21.4,22.3)
+
+    plt.figure()
+    kymo_selection.plot("rgb", adjustment=lk.ColorAdjustment(0, 98, mode="percentile"))
+
+Get the raw data (photon counts for each pixel) for the selected region::
+
+    selection_green = kymo_selection.get_image(channel = 'green')
+
+.. image:: figures/kymographs/kymograph_selection.png
+
+If the background has to be subtracted, choose a region without binding events as background::
+
+    background =  kymo["92.1s":"100s"].crop_by_distance(21.4,22.3)
+    
+    plt.figure()
+    background.plot("rgb", adjustment=lk.ColorAdjustment(0, 98, mode="percentile"))
+
+.. image:: figures/kymographs/background.png
+
+Subtract the background and sum over the vertical axis (along the width of the binding event) to obtain the photon counts over time::
+
+    background_mean = np.mean(background.get_image(channel = "green"))
+    photon_counts = np.sum(selection_green-background_mean, axis = 0)
+    time = np.arange(len(photon_counts))*kymo.line_time_seconds
+
+    plt.figure()
+    plt.plot(time, photon_counts)
+    plt.xlabel("time (s)")
+    plt.ylabel("Photon counts")
+    plt.title("Photon counts along binding event")
+
+.. image:: figures/kymographs/photon_counts.png
+
 Calibrating to base pairs
 -------------------------