titizheng
20 magnification
Hi， How can we ensure that the Whole Slide Images (WSIs) are at a 20x magnification? If they are not at 20x magnification, how should they be handled? Is there corresponding code available for this? Thank you！
You can obtain the corresponding magnification from the slide scanning metadata properties using the code below. The slide contain the magnification and other related metadata properties, which can be accessed through slide.properties using the openslide library. This includes:
Magnification (e.g., aperio.AppMag or openslide.mpp-x) Dimensions of the slide (e.g., width and height) Size information for different levels (e.g., slide.level_dimensions)
** def display_wsi_info_and_level(wsi_path, level): # Open the WSI file slide = openslide.open_slide(wsi_path) # Get the dimensions of the WSI width, height = slide.dimensions print("WSI Dimensions: {}x{}".format(width, height)) # Get the number of levels in the WSI num_levels = slide.level_count dimensions = slide.level_dimensions print("WSI Level Count:", num_levels) print("WSI Level Details:", dimensions) # Get WSI metadata and read related information if 'aperio.AppMag' in slide.properties.keys(): level_0_magnification = int(slide.properties['aperio.AppMag']) elif 'openslide.mpp-x' in slide.properties.keys(): level_0_magnification = 40 if int(np.floor(float(slide.properties['openslide.mpp-x']) * 10)) == 2 else 20 else: level_0_magnification = 40 # Output the magnification corresponding to level 0 print("Magnification for level_0:", level_0_magnification) magnification = 10 # Calculate the downsampling rate based on the level 0 magnification and the desired magnification, # e.g., if level 0 has a magnification of 40, and we want 5x, then the downsampling rate is 40/5=8 downsample = level_0_magnification / 5 # Get the level corresponding to the closest magnification for this downsampling rate level = slide.get_best_level_for_downsample(downsample) print("{}x magnification corresponds to Level_{}".format(magnification, level)) wsi_path = r'./dataset/BRCA/BRCA-slides/TCGA-5L-AAT1-01Z-00-DX1.F3449A5B-2AC4-4ED7-BF44-4C8946CDB47D.svs' selected_level = 2 display_wsi_info_and_level(wsi_path, selected_level)
**
