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.

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 input files), otherwise bounding boxes are omitted.

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 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.

.
├── 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