--- a
+++ b/docs/TA export.rst
@@ -0,0 +1,108 @@
+.. _Export_page:
+
+************************
+Whole Slide Image export
+************************
+
+There are videos detailing the whole slide image export process from start to finish at the :ref:`end of this page<page_examples>`.
+Below is a breakdown of each panel and button used in the examples.
+
+Tissue export window
+====================
+
+.. image:: images/Cut_application_screen.png
+
+The tissue export window is for exporting png images from whole slide files using a map of the array that is provided by the user -
+see :ref:`array map example<Input_page>`.
+
+#. Load WSI prompts a dialog box for the user to select a NDPI or SVS file.
+
+#. Load Excel this is a prompt to load the :ref:`excel map <Input_page>`.
+
+   * If the excel is named the same as the array and in the same directory,it will be loaded automatically. Otherwise this button can be used to load a different location.
+
+   * If this has happened then the button will turn green.
+
+   * This can also be used to reload the excel map at any point if the map has been changed by the user.
+
+#. Overlay of manually selected cores.
+
+   * This is applied after a user selection has been applied in panel number 5.
+
+   * It can also be used after the cores have been moved to update the window.
+
+#. Export cores should only be executed the user is satisfied that the cores are in the correct configuration.
+
+   * Export core command will disable user input and export the core png images to the WSI directory.
+
+#. Display window.
+
+   * Double click to add core.
+
+   * Spacebar to remove last point.
+
+   * You can drag pre-applied cores before or after applying the bounding boxes.
+
+#. Excel layout the recommended way to index cores is with the row names as the number and the column names as the
+   letter \(A6 col A row 6\) if you want to reverse this \(A6 row A col 6\) then uncheck the box when the window opens.
+
+#. *Save overlay image* determines whether or not to automatically save the image in the viewer (5).
+
+#. *Tab viewer window* is further explained in points 11-18.
+
+#. Image metadata for the WSI file.
+
+#. *Progress update panel* is where progress updates will appear.
+
+#. *Core diameter* is currently set to 6000 pixels which is similar bounding box size as a 1mm diameter tissue core.
+
+   * This value can be chosen before image export and you can see what the new selection looks like by selecting the
+     overlay cores button (3).
+
+#. Thresholding options.
+
+   * Choose the best threshold then proceed to 13.
+
+#. Gaussian blur shows the sigma value applied to the gaussian which must be applied after 12.
+
+#. Closing should be applied after 13 and stands for binary morphological closing.
+
+   * higher slider values will lead to a more closed mask.
+
+#. Removal of small objects from the mask gives the value of the minimum size to be removed.
+
+   * If you have very small tissue cores then this will need to be reduced.
+
+#. This applies the changes added in steps 12-15 and overlays the core images and labels.
+
+#. These are the settings for the first figure that is exported.
+
+   * This option will add a bounding box to the figure to denote the pathology of the core as either red or green.
+
+   * This will only work if the first tab of the xlsx file with the array contains a map indexed with N and T for normal and tumour, respectively.
+
+   * Please see the :ref:`array map example<Input_page>` for more indexing pathology details.
+
+#. If you increase this number, then it will increase the level that the images are taken from in the WSI.
+
+   * Increasing this will exponentially slow the program down so use sparingly.
+
+.. _page_examples:
+
+Example tissue array export workflow 1 - Auto threshold
+#######################################################
+
+.. raw:: html
+
+    <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 100%; height: auto; margin-bottom: 2em;">
+        <iframe src="https://www.youtube.com/embed/Bsop3Oi1Evg" frameborder="0" allowfullscreen style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"></iframe>
+    </div>
+
+Example tissue array export workflow 2 - Manual selection
+#########################################################
+
+.. raw:: html
+
+    <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 100%; height: auto; margin-bottom: 2em;">
+        <iframe src="https://www.youtube.com/embed/PCiH2Njfpso" frameborder="0" allowfullscreen style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"></iframe>
+    </div>