{
  "id": 579659,
  "title": "🪡 Correcting wrongly-quantized train tomograms",
  "url": "/competitions/byu-locating-bacterial-flagellar-motors-2025/discussion/579659",
  "author_name": "Bilzard",
  "post_date": "2025-05-19T10:45:15.275000",
  "votes": 12,
  "comment_count": 0,
  "views": 0,
  "content": "<p>As I reported earlier[1], it seems improper uint8 quantization seems to common on Cryo-ET datasets.<br>\nI also found few tomograms in train dataset contains such errors.</p>\n<p>I share notebook to correct this error.</p>\n<p>Notebook:<br>\n<a href=\"https://www.kaggle.com/code/tatamikenn/byu-correct-train-tomogram\" target=\"_blank\">https://www.kaggle.com/code/tatamikenn/byu-correct-train-tomogram</a></p>\n<p>Dataset:<br>\n<a href=\"https://www.kaggle.com/datasets/tatamikenn/byu-corrected-train-tomograms\" target=\"_blank\">https://www.kaggle.com/datasets/tatamikenn/byu-corrected-train-tomograms</a></p>\n<p><strong>Example Images</strong>:</p>\n<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F2bbb89a13e45ec042f1aca8e3d2ca479%2FScreenshot%202025-05-19%20at%2019.31.06.png?generation=1747651035939931&amp;alt=media\" alt=\"\"><br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F0bf47176d5649c77989754eff8c51081%2FScreenshot%202025-05-19%20at%2019.31.10.png?generation=1747651067531717&amp;alt=media\" alt=\"\"></p>\n<h2>Limitations</h2>\n<ul>\n<li>Since original tomogram already loses much information due to wrong quantization, corrected image has low color resolution</li>\n<li>This correction doesn't ensure perfect reconstruction of the original tomograms.</li>\n</ul>\n<h2>Reference</h2>\n<ol>\n<li><a href=\"https://www.kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025/discussion/575028\" target=\"_blank\">https://www.kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025/discussion/575028</a></li>\n</ol>",
  "messages": [
    {
      "id": 3205121,
      "postDate": "2025-05-19T10:45:15.277Z",
      "content": "<p>As I reported earlier[1], it seems improper uint8 quantization seems to common on Cryo-ET datasets.<br>\nI also found few tomograms in train dataset contains such errors.</p>\n<p>I share notebook to correct this error.</p>\n<p>Notebook:<br>\n<a href=\"https://www.kaggle.com/code/tatamikenn/byu-correct-train-tomogram\" target=\"_blank\">https://www.kaggle.com/code/tatamikenn/byu-correct-train-tomogram</a></p>\n<p>Dataset:<br>\n<a href=\"https://www.kaggle.com/datasets/tatamikenn/byu-corrected-train-tomograms\" target=\"_blank\">https://www.kaggle.com/datasets/tatamikenn/byu-corrected-train-tomograms</a></p>\n<p><strong>Example Images</strong>:</p>\n<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F2bbb89a13e45ec042f1aca8e3d2ca479%2FScreenshot%202025-05-19%20at%2019.31.06.png?generation=1747651035939931&amp;alt=media\" alt=\"\"><br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F0bf47176d5649c77989754eff8c51081%2FScreenshot%202025-05-19%20at%2019.31.10.png?generation=1747651067531717&amp;alt=media\" alt=\"\"></p>\n<h2>Limitations</h2>\n<ul>\n<li>Since original tomogram already loses much information due to wrong quantization, corrected image has low color resolution</li>\n<li>This correction doesn't ensure perfect reconstruction of the original tomograms.</li>\n</ul>\n<h2>Reference</h2>\n<ol>\n<li><a href=\"https://www.kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025/discussion/575028\" target=\"_blank\">https://www.kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025/discussion/575028</a></li>\n</ol>",
      "rawMarkdown": "As I reported earlier[1], it seems improper uint8 quantization seems to common on Cryo-ET datasets.\nI also found few tomograms in train dataset contains such errors.\n\nI share notebook to correct this error.\n\nNotebook:\nhttps://www.kaggle.com/code/tatamikenn/byu-correct-train-tomogram\n\nDataset:\nhttps://www.kaggle.com/datasets/tatamikenn/byu-corrected-train-tomograms\n\n**Example Images**:\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F2bbb89a13e45ec042f1aca8e3d2ca479%2FScreenshot%202025-05-19%20at%2019.31.06.png?generation=1747651035939931&alt=media)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F0bf47176d5649c77989754eff8c51081%2FScreenshot%202025-05-19%20at%2019.31.10.png?generation=1747651067531717&alt=media)\n\n## Limitations\n\n- Since original tomogram already loses much information due to wrong quantization, corrected image has low color resolution\n- This correction doesn't ensure perfect reconstruction of the original tomograms.\n\n## Reference\n\n1. https://www.kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025/discussion/575028",
      "votes": 12
    }
  ],
  "comments": [],
  "raw_markdown_by_id": {
    "3205121": "As I reported earlier[1], it seems improper uint8 quantization seems to common on Cryo-ET datasets.\nI also found few tomograms in train dataset contains such errors.\n\nI share notebook to correct this error.\n\nNotebook:\nhttps://www.kaggle.com/code/tatamikenn/byu-correct-train-tomogram\n\nDataset:\nhttps://www.kaggle.com/datasets/tatamikenn/byu-corrected-train-tomograms\n\n**Example Images**:\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F2bbb89a13e45ec042f1aca8e3d2ca479%2FScreenshot%202025-05-19%20at%2019.31.06.png?generation=1747651035939931&alt=media)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F4910466%2F0bf47176d5649c77989754eff8c51081%2FScreenshot%202025-05-19%20at%2019.31.10.png?generation=1747651067531717&alt=media)\n\n## Limitations\n\n- Since original tomogram already loses much information due to wrong quantization, corrected image has low color resolution\n- This correction doesn't ensure perfect reconstruction of the original tomograms.\n\n## Reference\n\n1. https://www.kaggle.com/competitions/byu-locating-bacterial-flagellar-motors-2025/discussion/575028"
  }
}