From each slide, 15 nonoverlapping fields for human lung tissue (HP patients n=9 and control subjects n=3) and 9 non-overlapping fields for mouse lung tissue (S. rectivirgula–treated n=9 and saline controls n=6) were captured using 40× objective and analyzed by using QuPath bioimage analysis software (https://qupath.github.io ).11 (link)
Images were taken using the Eclipse E600 Nikon microscope (Nikon, New York, USA) equipped with a DXM1200C digital camera (Nikon, New York, USA) and with the Nis Elements 3.0 software (Nikon, New York, USA). The brightfield digital image files were uploaded, a full-image annotation was created, and QuPath’s Positive Cell Detection algorithm was performed. The wand and brush tools were then used to annotate regions of tissue to define epithelium and immune cells. The measurement table was exported for statistical analysis (Percentage of positive cells = positive cells/total nuclei × 100). The mean percentage of all fields was calculated for each tissue sample and plot.
Images were taken using the Eclipse E600 Nikon microscope (Nikon, New York, USA) equipped with a DXM1200C digital camera (Nikon, New York, USA) and with the Nis Elements 3.0 software (Nikon, New York, USA). The brightfield digital image files were uploaded, a full-image annotation was created, and QuPath’s Positive Cell Detection algorithm was performed. The wand and brush tools were then used to annotate regions of tissue to define epithelium and immune cells. The measurement table was exported for statistical analysis (Percentage of positive cells = positive cells/total nuclei × 100). The mean percentage of all fields was calculated for each tissue sample and plot.
