Update of README file

README.md

@@ -9,8 +9,8 @@ image acquired by fluorescence microscopy. The program is available through a FI
 
 * [Citation.](#citation)
 * [Motivation](#motivation)
-* [Installation.](#installation)
 * [Description.](#description)
+* [Installation.](#installation)
 * [Example datasets.](#example-datasets)
 * [Usage.](#usage)
 
@@ -18,7 +18,7 @@ image acquired by fluorescence microscopy. The program is available through a FI
 
 ## Citation.
 
-If you use this work for your research, please cite the paper it is described in:
+If you use this work for your research, please cite our work:
 
 > __Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool.__
 >
@@ -32,21 +32,12 @@ The quantitative study of epithelium development by fluorescence microscopy requ
 epithelium to discard all potential contaminating structure (in terms of signal) surrounding it or the acquisition of
 all the epithelium adjacent structures allowing to have a more accurate state of the epithelium in its biological and
 physical environment. The latter approach requires to segment each structure separately. Most existing methods allow for
-the extraction of a single surface witch has to be smooth, and presenting a sufficiently high signal intensity and
+the extraction of a single surface which has to be smooth, and presenting a sufficiently high signal intensity and
 contrast and usually fail otherwise. These methods so far do not address the need to extract several surfaces of
 interest within the same volume. We developed Zellige, a tool allowing the automated extraction of a non-prescribed
 number of surfaces of varying inclination, contrast, and texture from a 3D image. The tool requires the adjustment of a
 small set of control parameters, for which we provide an intuitive interface implemented as a Fiji plugin.
 
-## Installation.
-
-As a FIJI plugin (https://fiji.sc/) ,Zellige can be installed directly within
-the [Fiji updater](https://imagej.net/ImageJ_Updater).
-
-In the `Manage update sites` window, check the `Zellige` plugin. Click the `Close` button, then the `Apply changes`
-button. After the plugin is downloaded, restart Fiji. The plugin can then be launched from the _Plugins >  Zellige_ menu
-item.
-
 ## Description.
 
 Zellige performs projection of multiple surfaces of interest on a 2D plane from a 3D image. For now, it can only be used
@@ -64,29 +55,28 @@ each channel, and is used to collect intensity in planes above or below the refe
 by a ∆z parameter, can be accumulated to generate a better projection, averaging the pixel values or taking the maximum
 value of these planes.
 
-## Example datasets
-
-https://zenodo.org/record/6376584
+## Installation.
 
-https://zenodo.org/record/6376594
+As a FIJI plugin (https://fiji.sc/) ,Zellige can be installed directly within
+the [Fiji updater](https://imagej.net/ImageJ_Updater).
 
-https://zenodo.org/record/6376582
+In the `Manage update sites` window, check the `Zellige` plugin. Click the `Close` button, then the `Apply changes`
+button. After the plugin is downloaded, restart Fiji. The plugin can then be launched from the _Plugins > Process >
+Zellige_ menu item.
 
-https://zenodo.org/record/6376566
+## Example datasets
 
-https://zenodo.org/record/6376542
+https://zenodo.org/communities/zellige/
 
 ## Usage
 
-After installation, the plugin is located in the `Plugins >` menu of Fiji. The Zellige window is divided in 3 parts
-corresponding to each step of the program. Its UI is a single window divided in 3 for each stage (selection,
-construction and projection):
+https://imagej.net/plugins/zellige
 
 ### Other projection tools.
 
 There are several other tools to generate this kind of projections:
 
-- Local Z projector, an ImageJ plugin :
+- Local Z projector, an ImageJ plugin: https://gitlab.pasteur.fr/iah-public/localzprojector
 - Stack Focuser, an ImageJ plugin: https://imagej.nih.gov/ij/plugins/stack-focuser.html
 - SurfCut, an Image macro: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0657-1
 - PreMosa, a standalone software: https://academic.oup.com/bioinformatics/article/33/16/2563/3104469