📂Output

All the results of the script would be saved in the results directory, and the structure for each of it will be as shown in the last screen.

Results

The folder is automatically generated by the Qupath batch analysis. For each slide, a text file is created containing the information of the cell detection.

Output in the results folder, a text file is created for each slide

Each detected object gets an ObjectID, an Object type a Classification, and a Parent. The classification is defined through the object classifier, giving us no cell (NoCell), immune-positive (PositiveCell), and immune-negative (NegativeCell) cells. The Parent for automatic tissue detection is Region whereas if manual-specific detection is performed the Parent differs accordingly.

The positivity rate could now be manually calculated from each .txt file. To speed up the process and make it more efficient we have created a script that automatically calculates the positivity rate for each slide linking the ID_Slidescanner with the ID_Sample. To create an Excel sheet as shown below please follow the ProcessingScan Package Tutorial.

Final output sheet