.. _Export_page:

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Whole Slide Image export

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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

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.. 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>