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