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docs: cleanup
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paulmueller committed Jan 27, 2020
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Expand Up @@ -22,7 +22,7 @@ Data analysis
-------------
To make data analysis easier, we first divide the dataset by copying the files
of the compliant gel (*PAAm_Compliant_\*.jpk-force*) and the stiff gel
(*PAAm_Stiff_\*.jpk-force*) into to two separate folders "compliant" and "stiff".
(*PAAm_Stiff_\*.jpk-force*) into two separate folders "compliant" and "stiff".


In PyJibe, we load each of the folders using *File | Open bulk data*. We
Expand Down Expand Up @@ -71,12 +71,12 @@ There are several things to note here:
*force-modulation* feedback mode. The gel is not probed in *contact* mode,
but in a mixture between contact mode and intermittend mode (See the
NanoWizard User Manual v. 4.2, sec. 5.7.). Maybe this ringing is not
visible for the compliant gels, because of the setpoint at 6nN (The setpoint
visible for the compliant gel, because of the setpoint at 6n N (The setpoint
likely defines the amplitude of the force-modulation feedback mode and for
the compliant gels, this amplitude is below the noise level).
the compliant gels, this amplitude might be below the noise level).

- Stiff gels get a better rating than compliant gels with the *zef18 + Extra
Trees* rating scheme (please see :ref:`the nanite rating workflow
- The stiff gel gets a better rating than the compliant gel with the *zef18 +
Extra Trees* rating scheme (please see :ref:`the nanite rating workflow
<nanite:sec_rating>` and :cite:`Mueller19nanite` for how rating works).
Of course, this observation is misleading - it nicely illustrates a limit
of machine learning. The *zef18* training set was created using zebrafish
Expand All @@ -88,7 +88,8 @@ There are several things to note here:
Results
-------
You might have realized that PyJibe creates the file
*pyjibe_fit_results_leaf.tsv* in each of the measurement folders. These
*pyjibe_fit_results_leaf.tsv* in each of the measurement folders (if the
*Autosave fit results as .tsv* check box is checked). These
files contain (amongst other things) the fit results of each curve. With
a simple Python script, we can visualize the Young's modulus of the two gels:

Expand Down Expand Up @@ -121,6 +122,6 @@ a simple Python script, we can visualize the Young's modulus of the two gels:

Comparison of the hydrogels. Note that the X axes are scaled differently.

The compliant hydrogel has a Young's modulus of 1090 ± 10 Pa and the stiff
hydrogel has a Young's modulus of 27680 ± 270 Pa. These values agree well
with the values we expected initially.
The compliant hydrogel has a Young's modulus of 1090 ± 10 Pa (mean ± SD) and
the stiff hydrogel has a Young's modulus of 27680 ± 270 Pa. These values agree
well with the values we expected initially.

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