--- a
+++ b/docs/Output files.rst
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+.. _Output_page:
+
+*******************
+Output from QuArray
+*******************
+
+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
+-----------------------------------------------------------
+
+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
+