update of README file

README.md

-# Zellige
+![Zellige_logo](src/main/resources/icons/Zellige_logo.png)
+<img src="doc/zellige_pipeline.jpg" width="150" height="150" alt="drawing"/>
+<img src= "doc/zellige_pipeline.jpg">
 
-## Workflow
+# Zellige : 3D fluorescence microscopic images surface extraction tool.
 
-The program takes a 3D stack as input and generates the projection of all surfaces contained in the 3D stack as 2D
-images. That process can be divided into 3 stages :
+Zellige is a software tool allowing the automated extraction of a non-prescribed number of various surfaces from a 3D
+image acquired by fluorescence microscopy. The program is available through a FIJI plugin.
 
-- first the selection of all the pixels belonging to any selectedPixels
-- second the regrouping of those selected pixels to produce a height map for each selectedPixels
-- third the use of each height map to extract a projection according to a given projection's method (only MIP for now).
+**Table of content.**
 
-![ZelligePipeline](doc/zellige_pipeline.jpg)
+* [Citation.](#citation)
+* [Motivation](#motivation)
+* [Installation.](#installation)
+* [Description.](#description)
+* [Example datasets.](#example-datasets)
+* [Usage.](#usage)
 
-## Build
++ [Other projection tools.](#other-projection-tools)
 
-````
+## Citation.
 
- mvn clean install
+If you use this work for your research, please cite the paper it is described in:
+
+> __Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool.__
+>
+> Céline Trébeau, Jacques Boutet de Monvel, Gizem Altay, Jean-Yves Tinevez, Raphaël Etournay
+>
+> bioRxiv 2022.04.05.485876; doi: https://doi.org/10.1101/2022.04.05.485876
+
+## Motivation
+
+The quantitative study of epithelium development by fluorescence microscopy requires either the dissection of the
+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
+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
+on 1-channel 3D images presenting one or several surfaces. The program takes a 3D stack as input and generates the
+projection of all surfaces contained in the 3D stack as 2D images. That process can be divided into 3 stages :
+
+![ZelligePipeline](doc/zellige_pipeline.jpg = 200 x 200)
+
+- first the selection of all the pixels belonging to any surface
+- second the regrouping of those selected pixels to produce a **height map** for each surface
+- third the use of each height map to extract a projection.
+
+The height-map is then used to extract a projection from the 3D image. A fixed offset can be specified separately for
+each channel, and is used to collect intensity in planes above or below the reference surface. Several planes, specified
+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
+https://zenodo.org/record/6376594
+https://zenodo.org/record/6376582
+https://zenodo.org/record/6376566
+https://zenodo.org/record/6376542
 
- ````
- 
 ## Usage
 
-The plugin is currently in development
-````
- 
-````
- 
-## Pipelines
- 
-https://gitlab.pasteur.fr/ctrebeau/zellige-core/-/pipelines
\ No newline at end of file
+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):
+
+### Other projection tools.
+
+There are several other tools to generate this kind of projections:
+
+- Local Z projector, an ImageJ plugin :
+- 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
+- Extended Depth of Field, an ImageJ plugin: http://bigwww.epfl.ch/demo/edf/
+- Min. Cost Z Surface, an ImageJ plugin: https://imagej.net/Minimum_Cost_Z_surface_Projection
+- FastSME and SME, MATLAB software for the extraction of smooth-manifold
+  structures: https://openaccess.thecvf.com/content_cvpr_2018_workshops/w44/html/Basu_FastSME_Faster_and_CVPR_2018_paper.html