.. _Input_page:

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Input files

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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

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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.