There are no important user methods for `epicell`. All the important information is already in the properties.

There are no important user methods for `epicell`. All the important information is already in the properties. Check the [documentation on properties](DeProjProperties.md).

### Secondary `epicell` methods.

...

...

@@ -200,8 +200,132 @@ The first output arguments `f3d` contains the ellipse parameter in cartesian for

The second argument `R` is the rotation matrix computed from the Euler angles.

## The `deproj` class methods.

A `deproj` instance has several interesting methods, that let you export and display the analysis results. In particular the plotting routines: you will most likely be adapting them to your needs with a bit of MATLAB.

In the following we suppose that `dpr` is an instance of `deproj`, for instance obtained by executing the a [self-contained example](RunExample.m) in this repository:

'First Euler angle for the cell plane (rotation around Z)'

```

And a table description:

```matlab

>>T.Properties.Description

ans=

'Data generated from DeProj software, exported on 21-Jul-2020 23:07:02.'

```

#### `to_file`

`to_file( obj, file_name, include_header )`

Exports results to a spreadsheet file.

If `file_name` has `.csv` as extension, the data is saved as a CSV file. If it has `.xlsx` as an extension, it is saved as an Excel spreadsheet. The boolean flag `include_header` specifies whether the file will have a header with column names and units.

Generate a figure with the cells area and perimeter. All the plots generated by the `plot_*` methods are 3D plots. The cells are drawn with their 3D coordinates and you can zoom, rotate, pan to make the curvature of the tissue appear.

The `scale_bar_length` parameter specifies what should be the length (in physical units) of the scale bar added to the bottom left of the plot. By default it is 10. The output arguments `[ hf, ax1, ax2 ]` are respectfully the handles to the figure created, to the top axes and to the bottom axes.

Generate a figure with the local plane orientation for each cell. This orientation is given as 3 Euler angles in the [ZX'Z'' convention](https://en.wikipedia.org/wiki/Euler_angles#Chained_rotations_equivalence).

- The first one, `alpha` is the orientation of the cell plane (top panel below). As an analogy, imaging you are facing a hill, the slope going up. The direction (south, west…) in which the slope is the largest is given by the angle `alpha`. On these figures we wrap the angle between 0º and 180º to and because of MATLAB convention, this angle is measured counterclockwise from the Y axis (so 90º corresponds to a slope going up in the east-west direction).

- The second one, `beta` measures the slope of this plane with XY plane (middle panel). A value of 0º indicates that the cell plane is parallel to XY.

- The third one , `gamma` measures the cell main orientation in the cell plane (bottom panel). Because the cell plane was rotated a first time by `alpha`, this angle does not give a result immediately usable.