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README.md

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+# ImaCytE
+
+ImaCytE is a tool developed for the interactive and data-driven exploration of Imaging Mass Cytometry data as presented in the paper "ImaCytE: Visual Exploration of Cellular Micro-environments for Imaging Mass Cytometry Data". 
+It is focused on the identification of the cell phenotypes that exist in the samples and the interactive exploration of their microenvironment. 
+
+### Cite:
+"to be added"
+
+## Getting started
+
+In case you have a Matlab 2016b or newer you can run ImaCytE from source code. 
+
+If you have an older version or you don't have a Matlab installed in your PC I can send you a standalone application of ImaCytE for Windows 7/10.
+
+### Using ImaCytE from source code
+
+* Please download the full repisotory and add it to your current direcotry. 
+
+* Run ImaCytE.m to start histoCAT from source
+
+### Loading data for analysis 
+
+* Select the Option menu
+
+* Click on the Load Data
+
+* Then you provide a **folder**. 
+In this folder should be **one subfolder for each sample** you want to load. 
+In each subfolder you must include a mutliple **".tiff"** file with all the markers as exported from MCD viewer and **"*_mask.tiff"** file which would be the cell mask
+
+### Contact
+
+Antonios Somarakis a.somarakis@lumc.nl