converted image appears black vertical stripes

[13512263278]

Operating system

Ubuntu 22.04.2 LTS (GNU/Linux 5.19.0-32-generic x86_64)

Platform

GNU/Linux 5.19.0-32-generic x86_64

OpenSlide Python version

1.4.1

OpenSlide version

4.0.0

Slide format

SVS

Issue details

I use openslide to convert my slice SVS file to PNG file, but the converted image appears black vertical stripes.

Here is my code： `def tif_to_png_with_openslide2(tif_image_path, png_output_path): try: # 使用 OpenSlide 打开大文件 slide = openslide.OpenSlide(tif_image_path) for key, value in slide.properties.items(): print(key, value) slide_data = slide.read_region((0, 0), 1, slide.level_dimensions[1]) slide_data = np.array(slide_data) r,g,b,a = cv2.split(slide_data) slide_data = cv2.merge([r,g,b]) cv2.imwrite(png_output_path, slide_data)

    print(f"Successfully converted {tif_image_path} to {png_output_path}")
except Exception as e:
    print(f"Error converting TIFF to PNG: {e}")

this is slide.properties:aperio.AppMag 40 aperio.MPP 0.253910 openslide.associated.thumbnail.height 543 openslide.associated.thumbnail.width 1204 openslide.comment Aperio Image Format 154112x69600 [0,0 154112x69600] (256x256) JPEG/RGB Q=60|AppMag = 40|MPP = 0.253910 openslide.level-count 2 openslide.level[0].downsample 1 openslide.level[0].height 69600 openslide.level[0].tile-height 256 openslide.level[0].tile-width 256 openslide.level[0].width 154112 openslide.level[1].downsample 8 openslide.level[1].height 8700 openslide.level[1].tile-height 256 openslide.level[1].tile-width 256 openslide.level[1].width 19264 openslide.mpp-x 0.25391000000000002 openslide.mpp-y 0.25391000000000002 openslide.objective-power 40 openslide.vendor aperio tiff.Artist KFBIO tiff.ImageDescription Aperio Image Format 154112x69600 [0,0 154112x69600] (256x256) JPEG/RGB Q=60|AppMag = 40|MPP = 0.253910 tiff.ResolutionUnit inch`

[13512263278]

this is my code .i try to two way to finish: `def tif_to_png_with_openslide2(tif_image_path, png_output_path): try: # 使用 OpenSlide 打开大文件 slide = openslide.OpenSlide(tif_image_path) for key, value in slide.properties.items(): print(key, value) slide_data = slide.read_region((0, 0), 1, slide.level_dimensions[1]) slide_data = np.array(slide_data) r,g,b,a = cv2.split(slide_data) slide_data = cv2.merge([r,g,b]) cv2.imwrite(png_output_path, slide_data)

    print(f"Successfully converted {tif_image_path} to {png_output_path}")
except Exception as e:
    print(f"Error converting TIFF to PNG: {e}")`
    

code 2: `def tif_to_png_with_openslide(tif_image_path, png_output_path): try: # 使用 OpenSlide 打开大文件 slide = openslide.OpenSlide(tif_image_path)

    # 指定缩略图的目标大小
    thumbnail_size = (2048, 2048)

    # 获取缩略图
    thumbnail = slide.get_thumbnail(thumbnail_size)

    # 将图像保存为 PNG 格式
    thumbnail.save(png_output_path)
    print(f"Successfully converted {tif_image_path} to {png_output_path}")
except Exception as e:
    print(f"Error converting TIFF to PNG: {e}")`

[bgilbert]

Your SVS file probably omits image tiles for empty portions of the slide. OpenSlide renders missing image tiles as transparent pixels, which you're seeing as black pixels because you're discarding the returned alpha channel.

The stripes are surprising though. Could you upload a sample slide that shows this behavior?

[13512263278]

Your SVS file probably omits image tiles for empty portions of the slide. OpenSlide renders missing image tiles as transparent pixels, which you're seeing as black pixels because you're discarding the returned alpha channel.

The stripes are surprising though. Could you upload a sample slide that shows this behavior?

Thank you very much. I have uploaded my SVS file。 ps: google account:[email protected] email:[email protected] file name: N006802-1-2.svs