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-# Refahi_etal_2020
+## Introduction
 
-Scripts and software used to produce the results in the manuscript "Flower".
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+Scripts and software used to produce the results in the manuscript "Flower".
+
+## Scripts and software
+
+We have collected the tools to produce the result in four folders following the
+outline of the paper. For an overview of the methods used, see the Methods section 
+of the paper.
+
+<p><i>segmentation_tracking</i> has information on the segmentation and tracking used
+to produce the data set for example shown in Figure 2 of the paper.</p>
+
+<p><i>registration</i> describes the method for registration of different flowers 
+onto each other (see e.g. Figure 3).</p>
+
+<p><i>expressionAnalysis</i> has the methods for analysing the spatiotemporal
+gene expression patterns of the early flower (e.g. Figures 4-5).</p>
+
+<p><i>geneRegulation</i> has the scripts to perform model prediction and hypothesis testing of the
+gene regulatory network (e.g. Figures 1 and 6).</p>
+
+<p><i>growthAnalysis</i> holds the scripts for analysing growth and anisotropy changes 
+within the dataset (e.g. Figures 7-9).</p>
+
+We have used outside tools, in-house tools, and python scripts. See further details 
+in the README files within the specific folders.
+
+## Contact
+
+yassin.refahi@inra.fr
+
+argyris.zardilis@slcu.cam.ac.uk
+
+henrik.jonsson@slcu.cam.ac.uk
+
+jan.traas@ens-lyon.fr
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