![\"\"](\"https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F621560%2Fbd52e65119ae3041ef5f4111a889a890%2F70256626a66f83e38b69a88a68967130_level0_.png?generation=1591790740324197&alt=media\")
\n\n slide_image = slide.read_region((0, 0), 1, slide.level_dimensions[1]).convert(\"RGB\")\n\n![\"\"](\"https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F621560%2F42ad067f4af8f01cb7d804c52fe210cf%2F70256626a66f83e38b69a88a68967130_level1_.png?generation=1591790767041420&alt=media\")
Wondering if anybody else has noticed issues with Openslide?
\n\nFor certain images (typically the very large ones) I get areas of blanks in the images when I open level 1, but not level 0.
\n\nTake 70256626a66f83e38b69a88a68967130.tiff for example:\n\nslide = openslide.open_slide('/kaggle/input/prostate-cancer-grade-assessment/train_images/70256626a66f83e38b69a88a68967130.tiff')\nslide_image = slide.read_region((0, 0), 0, slide.level_dimensions[0]).convert(\"RGB\")\n
\n\n slide_image = slide.read_region((0, 0), 1, slide.level_dimensions[1]).convert(\"RGB\")\n\n
There are many files where this is the case. I can't check out whether skimage / imageio give the same issues as I can't get them to work in kernels. Has anyone else come across this? Do you know if it is a problem with the file rather than the openslide package? (i.e. does it work in skimage/imageio)?
\n\nThanks
", "messages": [ { "id": 880598, "postDate": "2020-06-10T12:19:51.377Z", "content": "Wondering if anybody else has noticed issues with Openslide?
\n\nFor certain images (typically the very large ones) I get areas of blanks in the images when I open level 1, but not level 0.
\n\nTake 70256626a66f83e38b69a88a68967130.tiff for example:\n\nslide = openslide.open_slide('/kaggle/input/prostate-cancer-grade-assessment/train_images/70256626a66f83e38b69a88a68967130.tiff')\nslide_image = slide.read_region((0, 0), 0, slide.level_dimensions[0]).convert(\"RGB\")\n
\n\n slide_image = slide.read_region((0, 0), 1, slide.level_dimensions[1]).convert(\"RGB\")\n\n
There are many files where this is the case. I can't check out whether skimage / imageio give the same issues as I can't get them to work in kernels. Has anyone else come across this? Do you know if it is a problem with the file rather than the openslide package? (i.e. does it work in skimage/imageio)?
\n\nThanks
", "rawMarkdown": "Wondering if anybody else has noticed issues with Openslide?\n\nFor certain images (typically the very large ones) I get areas of blanks in the images when I open level 1, but not level 0.\n\nTake 70256626a66f83e38b69a88a68967130.tiff for example:\n```\nslide = openslide.open_slide('/kaggle/input/prostate-cancer-grade-assessment/train_images/70256626a66f83e38b69a88a68967130.tiff')\nslide_image = slide.read_region((0, 0), 0, slide.level_dimensions[0]).convert(\"RGB\")\n```\n\n\n```\n slide_image = slide.read_region((0, 0), 1, slide.level_dimensions[1]).convert(\"RGB\")\n```\n\n\nThere are many files where this is the case. I can't check out whether skimage / imageio give the same issues as I can't get them to work in kernels. Has anyone else come across this? Do you know if it is a problem with the file rather than the openslide package? (i.e. does it work in skimage/imageio)?\n\nThanks", "votes": 1 }, { "id": 880685, "postDate": "2020-06-10T13:48:19.233Z", "content": "I wasn't able to reproduce this problem with the latest docker. What are you using for displaying the cases? Maybe you can share a notebook to show where the problem occurs.
", "rawMarkdown": "I wasn't able to reproduce this problem with the latest docker. What are you using for displaying the cases? Maybe you can share a notebook to show where the problem occurs.", "replies": [ { "id": 880727, "postDate": "2020-06-10T14:21:56.867Z", "content": "Ah, could be that. I'll play around and see. Thanks
", "rawMarkdown": "Ah, could be that. I'll play around and see. Thanks" } ] }, { "id": 880636, "postDate": "2020-06-10T13:04:25.010Z", "content": "Update on this: I managed to get imageio working and I'm not seeing the same issue for the sample file above when using that.
", "rawMarkdown": "Update on this: I managed to get imageio working and I'm not seeing the same issue for the sample file above when using that." } ], "comments": [ { "id": 880685, "author_name": "Wouter Bulten", "author_url": "", "post_date": "2020-06-10T13:48:19.233000", "content": "I wasn't able to reproduce this problem with the latest docker. What are you using for displaying the cases? Maybe you can share a notebook to show where the problem occurs.
", "votes": 0, "replies": [ { "id": 880727, "author_name": "fergusoci", "author_url": "", "post_date": "2020-06-10T14:21:56.867000", "content": "Ah, could be that. I'll play around and see. Thanks
", "votes": 0, "replies": [] } ] }, { "id": 880636, "author_name": "fergusoci", "author_url": "", "post_date": "2020-06-10T13:04:25.010000", "content": "Update on this: I managed to get imageio working and I'm not seeing the same issue for the sample file above when using that.
", "votes": 0, "replies": [] } ], "raw_markdown_by_id": { "880598": "Wondering if anybody else has noticed issues with Openslide?\n\nFor certain images (typically the very large ones) I get areas of blanks in the images when I open level 1, but not level 0.\n\nTake 70256626a66f83e38b69a88a68967130.tiff for example:\n```\nslide = openslide.open_slide('/kaggle/input/prostate-cancer-grade-assessment/train_images/70256626a66f83e38b69a88a68967130.tiff')\nslide_image = slide.read_region((0, 0), 0, slide.level_dimensions[0]).convert(\"RGB\")\n```\n\n\n```\n slide_image = slide.read_region((0, 0), 1, slide.level_dimensions[1]).convert(\"RGB\")\n```\n\n\nThere are many files where this is the case. I can't check out whether skimage / imageio give the same issues as I can't get them to work in kernels. Has anyone else come across this? Do you know if it is a problem with the file rather than the openslide package? (i.e. does it work in skimage/imageio)?\n\nThanks", "880685": "I wasn't able to reproduce this problem with the latest docker. What are you using for displaying the cases? Maybe you can share a notebook to show where the problem occurs.", "880636": "Update on this: I managed to get imageio working and I'm not seeing the same issue for the sample file above when using that." } }