new documentation added

GiorgiaTortora · Nov 7, 2023 · 6d3c399 · 6d3c399
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diff --git a/README.md b/README.md
@@ -46,7 +46,7 @@ To install latest development version :
 
 ## Usage
 
-Detailed instructions on how to use the napari-roi-registration plugin can be found at https://github.com/GiorgiaTortora/napari-roi-registration/blob/main/docs/napari-roi-registration_guide.pdf.
+A detailed guide which shows in detail how to use the widgets of the napari-roi-registration plugin and how to properly choose the parameters can be found [here].
 
 ### Registration Widget
 
@@ -99,6 +99,7 @@ If you encounter any problems, please [file an issue] along with a detailed desc
 [Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
 [Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
 [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+[here]: https://github.com/GiorgiaTortora/napari-roi-registration/blob/main/docs/index.md
 
 [file an issue]: https://github.com/GiorgiaTortora/napari-roi-registration/issues
 

diff --git a/docs/index.md b/docs/index.md
@@ -17,9 +17,7 @@ The Background Widget allows a pre-processing of data, and it is typically usefu
 1. Open the image you want to correct in the napari viewer. If you open more than one image in the viewer, select the image you want to correct in the image menu of the Background Widget. 
 
 ![raw](https://github.com/GiorgiaTortora/napari-roi-registration/blob/main/images/before_sub.png)
-<figcaption>In the red ellipse on top right, the image menu of the background widget.</figcaption>
-</figure>  
-
+
 2. Create a new labels layer and draw a label on one frame of your stack on the area where you want to calculate the background. The background will be calculated as the mean intensity of the pixels under the drawn label.
 
 ![raw](https://github.com/GiorgiaTortora/napari-roi-registration/blob/main/images/background.png)
@@ -90,7 +88,7 @@ The Processing Widget measures ROIs displacements and extracts the average inten
 If **plot results** is selected, plots of displacement vs time index and mean intensity vs time index will appear in the console.  
 Choosing the **save results** option, an excel file containing ROIs positions, displacements, and intensities will be saved. 
 
-[raw](https://github.com/GiorgiaTortora/napari-roi-registration/blob/main/images/plots.png) 
+![raw](https://github.com/GiorgiaTortora/napari-roi-registration/blob/main/images/plots.png)
 
 
 
diff --git a/docs/napari-roi-registration_guide.pdf b/docs/napari-roi-registration_guide.pdf