.. _Output_page:

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Output from QuArray

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Tissue core threshold output

============================

.. note::

   The outputs of the tissue core export process are as follows. They are all saved into the same location in the

   whole slide image export file.

1. Whole core images - indexed with coordinates in the file name

----------------------------------------------------------------

Image of the selection panel

----------------------------

This will be created when overlay cores is pressed.

.. Image:: images/wsi_001_split_overlay.tiff

2. Figure containing images of all tissue cores in an array

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An example of such a figure is given below. A bounding box appears (e.g. green or red) if a pathology/condition map is

included in (see :ref:`input files<Input_page>`), otherwise bounding boxes are omitted.

.. Image:: images/wsi_001_split_layoutfig.tiff

3. Image metadata in JSON format

--------------------------------

The following fields are included.

:path: path of the whole slide image

:coordinates: list of tuple coordinates in the whole slide image

:cores: list of strings to denote core names

:diameter: int for the number of pixels in the image

:scale_index: float to show the scale index between low and high WSI levels

:lowlevel: int to show the level that the low magnification file was taken from

:arrayshape: tuple of the shape of the tissue array in col row format

Chromogen measurement output

============================

The output of the chromogen (e.g. DAB) measurement window is a single excel file (.xlsx) which contains measurements of

multiple parameters from each tissue core in the input folder.

The data is organised in a single row for the measurements for tissue each core image.

The column titles and data description appear as follows:

:CoreName: The file name of the analysed tissue image

:AMTsignal: the total number of pixels that contain 'signal' in the image\, Also termed coverage

:Mean_intensity: The mean average of the pixel values in the threshold image

:Standard_Dev_intensity: The standard deviation of the pixel values in the threshold image

:AMTtissue: The total amount of tissue in the image \(calculation provided in the :ref:`measurements page<Measurements_page>`

:AFperAMTT: The AMTsignal divided by the amount of tissue

:Mean_Intensity_perAMTT: The Mean_intensity divided by the amount of tissue

:SD_Intensity_perAMTT: The Standard_Dev_intensity divided by the amount of tissue

Output file structure

=====================

Below is an example of what the file structure could look like for an end to end project after running image export and

chromogen analysis.

.. code-block:: bash

   .

   ├── wsi_001.ndpi

   ├── wsi_001.xlsx

   └── wsi_001_split

       ├── CoreAnalysis_WSI_001.xlsx

       ├── wsi_001_split_A1.png

       ├── wsi_001_split_B1.png

       ├── wsi_001_split_C1.png

       ├── wsi_001_split_D1.png

       ├── wsi_001_split_layoutfig.tiff

       ├── wsi_001_split_metadata.json

       └── wsi_001_split_overlay.tiff