docs: add surface calibration example to the docs

lumicks · Oct 29, 2024 · 17e9aae · 17e9aae
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diff --git a/changelog.md b/changelog.md
@@ -17,7 +17,7 @@
 * Added parameter `titles` to customize title of each subplot in [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
 * Added [`KymoTrack.sample_from_channel()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrack.html#lumicks.pylake.kymotracker.kymotrack.KymoTrack.sample_from_channel) to downsample channel data to the time points of a kymotrack.
 * Added support for file names with spaces in [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi).
-* Added [`lk.touchdown()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.touchdown.html#lumicks.pylake.touchdown) to find the height above the surface using the axial force signal.
+* Added [`lk.touchdown()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.touchdown.html#lumicks.pylake.touchdown) to find the height above the surface using the axial force signal and added an example notebook demonstrating surface calibration.
 
 ## v1.5.3 | 2024-10-29
 

diff --git a/docs/api.rst b/docs/api.rst
@@ -42,6 +42,7 @@ Force calibration
     force_calibration.power_spectrum.PowerSpectrum
     force_calibration.power_spectrum_calibration.CalibrationResults
     force_calibration.calibration_models.DiodeCalibrationModel
+    force_calibration.touchdown.TouchdownResult
 
     :template: function.rst
 
@@ -50,6 +51,7 @@ Force calibration
     fit_power_spectrum
     viscosity_of_water
     density_of_water
+    touchdown
     coupling_correction_2d
 
 

diff --git a/docs/examples/index.rst b/docs/examples/index.rst
@@ -22,4 +22,5 @@ For all of the examples, it is assumed that the following lines precede any othe
     cas9_kymotracking/cas9_kymotracking
     hairpin_fitting/hairpin_unfolding
     droplet_fusion/droplet_fusion
+    surface_calibration/surface_calibration.rst
     bead_coupling/coupling
diff --git a/docs/examples/surface_calibration/ac_drag.png b/docs/examples/surface_calibration/ac_drag.png
diff --git a/docs/examples/surface_calibration/ac_pc_no_height.png b/docs/examples/surface_calibration/ac_pc_no_height.png
diff --git a/docs/examples/surface_calibration/ac_pc_with_height.png b/docs/examples/surface_calibration/ac_pc_with_height.png
diff --git a/docs/examples/surface_calibration/interference.png b/docs/examples/surface_calibration/interference.png
diff --git a/docs/examples/surface_calibration/surface_calibration.rst b/docs/examples/surface_calibration/surface_calibration.rst
diff --git a/docs/examples/surface_calibration/touchdown.png b/docs/examples/surface_calibration/touchdown.png
diff --git a/docs/examples/surface_calibration/widget_surf.png b/docs/examples/surface_calibration/widget_surf.png
diff --git a/docs/refs.bib b/docs/refs.bib
@@ -32,6 +32,28 @@ @article{Kaczmarczyk2022
   doi = {10.1038/s41467-022-33503-6}
 }
 
+@article{neuman2004optical,
+  title={Optical trapping},
+  author={Neuman, Keir C and Block, Steven M},
+  journal={Review of scientific instruments},
+  volume={75},
+  number={9},
+  pages={2787--2809},
+  year={2004},
+  publisher={American Institute of Physics}
+}
+
+@article{neuman2005measurement,
+  title={Measurement of the effective focal shift in an optical trap},
+  author={Neuman, Keir C and Abbondanzieri, Elio A and Block, Steven M},
+  journal={Optics letters},
+  volume={30},
+  number={11},
+  pages={1318--1320},
+  year={2005},
+  publisher={Optica Publishing Group}
+}
+
 @article{Kochaniak2009,
   author = {Kochaniak, A B and Habuchi, S and Loparo, J J and Chang D J and Cimprich K A and Walter J C and van Oijen A M},
   title = {Proliferating Cell Nuclear Antigen Uses Two Distinct Modes to Move along DNA},