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+.. _Input_page:
+
+***********
+Input files
+***********
+
+Whole Slide Image files
+=======================
+
+  .. note::
+     An example Tissue Array is hosted
+     `here <https://emckclac-my.sharepoint.com/:f:/g/personal/k1472221_kcl_ac_uk/EutLIT4yc3BIlmNdUnDzLNAB0AcR1qc99Pvf8w-yCcmj_A?e=LXunb4>`_.
+     The file contains a previously analyzed cancer tissue array (Arthurs et al, Sci Rep 2020) and mock data file.
+
+Supported Formats
+-----------------
+
+The program now supports whole slide images in the following vendors:
+
+* Hamamatsu (.ndpi, .vms, .vmu)
+* Aperio (.svs, .tif)
+* Leica (.scn)
+* Philips (.tiff)
+* Sakura (.svslide)
+* Generic tiled TIFF (.tif)
+* MIRAX (.mrxs)
+* Trestle (.tif)
+* Ventana (.bif, .bif)
+
+An example image of a WSI .ndpi file with tissue cores stained with DAB is given below:
+
+.. image:: images/example_ndpi.png
+
+Each core in this example is 1mm in diameter (the core diameter or number of cores is not a limitation for QuArray application). Scale bar is 1mm.
+
+Tissue array map file
+=====================
+
+A spreadsheet (Excel *.xlsx) file acts as a map of the array.
+
+The spreadsheet can also contain indexed information that is used for downstream analysis such as sample ID,
+sample details (e.g. date of sample collection, type) and categories (e.g. normal or diseased).
+
+File locations
+==============
+
+If the WSI file and the tissue array map file are saved in the same directory with the same name
+then the array map will be loaded automatically when the WSI file is loaded. Otherwise, the user load the map file
+separately.
+
+Here is an example of a normal tree file structure containing the WSI file and the index file.
+
+.. code-block:: bash
+
+   .
+   ├── WSI.ndpi
+   └── WSI.xlsx
+
+When the images are exported a new directory will be created inside the root to host output files.
+
+User interface
+==============
+
+.. image:: images/Pathology_maps.png
+
+Left - Image of the first tab.
+
+Right - Image of the second tab.
+
+The first tab contains 1 where a core is present and 0 where there is no core. There should be nothing in the rest
+of the document.
+
+The second tab contains pathology info and is used to make a figure if needed. This is not necessary to run the
+program. The tab does not have to be named *Pathology* but should be in the second tab location. T and N stand for Tumour
+and Normal respectively.
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