{
  "id": 552177,
  "title": "Does anyone know about the absolute size/diameter of the target molecules?",
  "url": "/competitions/czii-cryo-et-object-identification/discussion/552177",
  "author_name": "",
  "post_date": "2024-12-18T03:57:40.197093Z",
  "votes": 3,
  "comment_count": 2,
  "views": 0,
  "content": "<p>In the reference doc (<a href=\"https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1.full#T1)\" target=\"_blank\">https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1.full#T1)</a>, it seems like 80S ribosome's diameter is about 25nm? but curious whether we have more precise diameter measures of each target particles?</p>\n<p>Thanks!</p>",
  "messages": [
    {
      "id": "3074771",
      "postDate": "12/18/2024 03:57:40",
      "content": "<p>In the reference doc (<a href=\"https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1.full#T1)\" target=\"_blank\">https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1.full#T1)</a>, it seems like 80S ribosome's diameter is about 25nm? but curious whether we have more precise diameter measures of each target particles?</p>\n<p>Thanks!</p>",
      "rawMarkdown": "In the reference doc (https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1.full#T1), it seems like 80S ribosome's diameter is about 25nm? but curious whether we have more precise diameter measures of each target particles?\n\nThanks!",
      "votes": null
    },
    {
      "id": "3075018",
      "postDate": "12/18/2024 11:00:09",
      "content": "<p>Hi. The radius provided by competition for ribosomes is 150A, what is 30nm diameter. Pretty precise in my opinion considering the scale of the particles. Also molecules are not perfectly spherical and not rigit, as more bonds they have more flexible they are. So I wouldn't worry about search more precise measures than the ones you could experimentally find to get better general results for your model.</p>",
      "rawMarkdown": "Hi. The radius provided by competition for ribosomes is 150A, what is 30nm diameter. Pretty precise in my opinion considering the scale of the particles. Also molecules are not perfectly spherical and not rigit, as more bonds they have more flexible they are. So I wouldn't worry about search more precise measures than the ones you could experimentally find to get better general results for your model.",
      "votes": null
    },
    {
      "id": "3075213",
      "postDate": "12/18/2024 16:27:20",
      "content": "<p>You can always figure it out yourself.  Here's all of the images for each particle of TS_83_6 added together with the declared radius indicated.  (You can find the declared radii in the pinned notebooks. i.e. BlobDetector)</p>\n<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F10704200%2Fe3a5682e20c5c81454d650f5e5b9c255%2Fcomposite-particles.png?generation=1734538895417835&amp;alt=media\" alt=\"\"></p>\n<p>Note that this is when looking straight onto the x, y plane.  The particles are elongated along the z-axis which you can see a discussion of here:</p>\n<p><a href=\"https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization\" target=\"_blank\">https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization</a></p>\n<p>I would think the actual radius vs. what works best for an ML model might not be the same.</p>",
      "rawMarkdown": "You can always figure it out yourself.  Here's all of the images for each particle of TS_83_6 added together with the declared radius indicated.  (You can find the declared radii in the pinned notebooks. i.e. BlobDetector)\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F10704200%2Fe3a5682e20c5c81454d650f5e5b9c255%2Fcomposite-particles.png?generation=1734538895417835&alt=media)\n\nNote that this is when looking straight onto the x, y plane.  The particles are elongated along the z-axis which you can see a discussion of here:\n\n[https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization](https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization)\n\nI would think the actual radius vs. what works best for an ML model might not be the same.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3075018,
      "author_name": "sacuscreed",
      "author_url": "",
      "post_date": "12/18/2024 11:00:09",
      "content": "<p>Hi. The radius provided by competition for ribosomes is 150A, what is 30nm diameter. Pretty precise in my opinion considering the scale of the particles. Also molecules are not perfectly spherical and not rigit, as more bonds they have more flexible they are. So I wouldn't worry about search more precise measures than the ones you could experimentally find to get better general results for your model.</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 3075213,
      "author_name": "davidlist",
      "author_url": "",
      "post_date": "12/18/2024 16:27:20",
      "content": "<p>You can always figure it out yourself.  Here's all of the images for each particle of TS_83_6 added together with the declared radius indicated.  (You can find the declared radii in the pinned notebooks. i.e. BlobDetector)</p>\n<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F10704200%2Fe3a5682e20c5c81454d650f5e5b9c255%2Fcomposite-particles.png?generation=1734538895417835&amp;alt=media\" alt=\"\"></p>\n<p>Note that this is when looking straight onto the x, y plane.  The particles are elongated along the z-axis which you can see a discussion of here:</p>\n<p><a href=\"https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization\" target=\"_blank\">https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization</a></p>\n<p>I would think the actual radius vs. what works best for an ML model might not be the same.</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "3074771": "In the reference doc (https://www.biorxiv.org/content/10.1101/2024.11.04.621686v1.full#T1), it seems like 80S ribosome's diameter is about 25nm? but curious whether we have more precise diameter measures of each target particles?\n\nThanks!",
    "3075018": "Hi. The radius provided by competition for ribosomes is 150A, what is 30nm diameter. Pretty precise in my opinion considering the scale of the particles. Also molecules are not perfectly spherical and not rigit, as more bonds they have more flexible they are. So I wouldn't worry about search more precise measures than the ones you could experimentally find to get better general results for your model.",
    "3075213": "You can always figure it out yourself.  Here's all of the images for each particle of TS_83_6 added together with the declared radius indicated.  (You can find the declared radii in the pinned notebooks. i.e. BlobDetector)\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F10704200%2Fe3a5682e20c5c81454d650f5e5b9c255%2Fcomposite-particles.png?generation=1734538895417835&alt=media)\n\nNote that this is when looking straight onto the x, y plane.  The particles are elongated along the z-axis which you can see a discussion of here:\n\n[https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization](https://www.kaggle.com/code/davidlist/experiment-ts-6-4-visualization)\n\nI would think the actual radius vs. what works best for an ML model might not be the same."
  },
  "source": "meta"
}