{
  "id": 68101,
  "title": "Confocal microscopy settings",
  "url": "/competitions/human-protein-atlas-image-classification/discussion/68101",
  "author_name": "",
  "post_date": "2018-10-09T10:51:07.354201500Z",
  "votes": 5,
  "comment_count": 4,
  "views": 0,
  "content": "<p>Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?</p>\n\n<p>I think \"absolute\" intensities could be informative of subcellular localisation, and more critically prevent noise amplification from normalising to the maximum intensity per picture (irrespective of the channel), which is a widespread practice in CNN modeling.</p>\n\n<p>Everyone else, any thoughts?</p>",
  "messages": [
    {
      "id": "401049",
      "postDate": "10/09/2018 10:51:07",
      "content": "<p>Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?</p>\n\n<p>I think \"absolute\" intensities could be informative of subcellular localisation, and more critically prevent noise amplification from normalising to the maximum intensity per picture (irrespective of the channel), which is a widespread practice in CNN modeling.</p>\n\n<p>Everyone else, any thoughts?</p>",
      "rawMarkdown": "Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?\n\nI think \"absolute\" intensities could be informative of subcellular localisation, and more critically prevent noise amplification from normalising to the maximum intensity per picture (irrespective of the channel), which is a widespread practice in CNN modeling.\n\nEveryone else, any thoughts?",
      "votes": null
    },
    {
      "id": "401234",
      "postDate": "10/09/2018 16:50:04",
      "content": "<blockquote>\n  <p>Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?</p>\n</blockquote>\n\n<p>To all your questions: I don't think so. Even if they used the same instrument and the settings, there are different cells which do not express proteins equally well. Various proteins do not over-express equally even when all other conditions are the same.</p>\n\n<p>I don't think that absolute intensities carry any information regarding localization. Cells that have grown longer will typically have a stronger signal. Setting a microscope gain differently will affect the signal. The exact field of cells used for imaging matters as well.</p>\n\n<p>It is a binary choice. The signal is there or not, as its intensity can be explained by a variety of factors that have nothing to do with cellular localization.</p>",
      "rawMarkdown": "&gt; Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?\n\nTo all your questions: I don't think so. Even if they used the same instrument and the settings, there are different cells which do not express proteins equally well. Various proteins do not over-express equally even when all other conditions are the same.\n\nI don't think that absolute intensities carry any information regarding localization. Cells that have grown longer will typically have a stronger signal. Setting a microscope gain differently will affect the signal. The exact field of cells used for imaging matters as well.\n\nIt is a binary choice. The signal is there or not, as its intensity can be explained by a variety of factors that have nothing to do with cellular localization.",
      "votes": null
    },
    {
      "id": "401547",
      "postDate": "10/10/2018 08:56:29",
      "content": "<p>Hi Francisco, thanks for your feedback!</p>\n\n<blockquote>\n  <p>To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?</p>\n</blockquote>\n\n<p>The images were not captured on the same instrument, although we've used the same instrument model for all images. Most settings are the same but not all, and particularly not laser and detector settings. So I don't think that signal intensity is comparable across all images.</p>",
      "rawMarkdown": "Hi Francisco, thanks for your feedback!\n\n&gt; To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?\n\nThe images were not captured on the same instrument, although we've used the same instrument model for all images. Most settings are the same but not all, and particularly not laser and detector settings. So I don't think that signal intensity is comparable across all images.",
      "votes": null
    },
    {
      "id": "402745",
      "postDate": "10/12/2018 08:27:02",
      "content": "<p>Thank you, that answers my question!</p>",
      "rawMarkdown": "Thank you, that answers my question!",
      "votes": null
    },
    {
      "id": "402749",
      "postDate": "10/12/2018 08:41:53",
      "content": "<p>Hi Tilii. Yes, the fact that different cell types are used complicates things, and I agree it might be that they do not express proteins equally well. As for cells that have grown longer having stronger signal, I disagree in the sense that the light irradiating the cells focuses on focal planes. Here is an example using a pollen grain.\n<img src=\"https://static1.olympus-lifescience.com/data/olympusmicro/primer/techniques/confocal/images/confocalintrofigure6.jpg?rev=E606\" alt=\"https://www.olympus-lifescience.com\"></p>\n\n<p>However, I have seen some images that barely show anything in green, and in those situations intensity normalisation is bound to increase noise.</p>",
      "rawMarkdown": "Hi Tilii. Yes, the fact that different cell types are used complicates things, and I agree it might be that they do not express proteins equally well. As for cells that have grown longer having stronger signal, I disagree in the sense that the light irradiating the cells focuses on focal planes. Here is an example using a pollen grain.\n![https://www.olympus-lifescience.com][1]\n\nHowever, I have seen some images that barely show anything in green, and in those situations intensity normalisation is bound to increase noise.\n\n\n  [1]: https://static1.olympus-lifescience.com/data/olympusmicro/primer/techniques/confocal/images/confocalintrofigure6.jpg?rev=E606",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 401234,
      "author_name": "tilii7",
      "author_url": "",
      "post_date": "10/09/2018 16:50:04",
      "content": "<blockquote>\n  <p>Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?</p>\n</blockquote>\n\n<p>To all your questions: I don't think so. Even if they used the same instrument and the settings, there are different cells which do not express proteins equally well. Various proteins do not over-express equally even when all other conditions are the same.</p>\n\n<p>I don't think that absolute intensities carry any information regarding localization. Cells that have grown longer will typically have a stronger signal. Setting a microscope gain differently will affect the signal. The exact field of cells used for imaging matters as well.</p>\n\n<p>It is a binary choice. The signal is there or not, as its intensity can be explained by a variety of factors that have nothing to do with cellular localization.</p>",
      "votes": null,
      "replies": [
        {
          "id": 402749,
          "author_name": "monogenea",
          "author_url": "",
          "post_date": "10/12/2018 08:41:53",
          "content": "<p>Hi Tilii. Yes, the fact that different cell types are used complicates things, and I agree it might be that they do not express proteins equally well. As for cells that have grown longer having stronger signal, I disagree in the sense that the light irradiating the cells focuses on focal planes. Here is an example using a pollen grain.\n<img src=\"https://static1.olympus-lifescience.com/data/olympusmicro/primer/techniques/confocal/images/confocalintrofigure6.jpg?rev=E606\" alt=\"https://www.olympus-lifescience.com\"></p>\n\n<p>However, I have seen some images that barely show anything in green, and in those situations intensity normalisation is bound to increase noise.</p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 401547,
      "author_name": "martinhjelmare",
      "author_url": "",
      "post_date": "10/10/2018 08:56:29",
      "content": "<p>Hi Francisco, thanks for your feedback!</p>\n\n<blockquote>\n  <p>To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?</p>\n</blockquote>\n\n<p>The images were not captured on the same instrument, although we've used the same instrument model for all images. Most settings are the same but not all, and particularly not laser and detector settings. So I don't think that signal intensity is comparable across all images.</p>",
      "votes": null,
      "replies": [
        {
          "id": 402745,
          "author_name": "monogenea",
          "author_url": "",
          "post_date": "10/12/2018 08:27:02",
          "content": "<p>Thank you, that answers my question!</p>",
          "votes": null,
          "replies": []
        }
      ]
    }
  ],
  "raw_markdown_by_id": {
    "401049": "Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?\n\nI think \"absolute\" intensities could be informative of subcellular localisation, and more critically prevent noise amplification from normalising to the maximum intensity per picture (irrespective of the channel), which is a widespread practice in CNN modeling.\n\nEveryone else, any thoughts?",
    "401234": "&gt; Hi guys, interesting competition. To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?\n\nTo all your questions: I don't think so. Even if they used the same instrument and the settings, there are different cells which do not express proteins equally well. Various proteins do not over-express equally even when all other conditions are the same.\n\nI don't think that absolute intensities carry any information regarding localization. Cells that have grown longer will typically have a stronger signal. Setting a microscope gain differently will affect the signal. The exact field of cells used for imaging matters as well.\n\nIt is a binary choice. The signal is there or not, as its intensity can be explained by a variety of factors that have nothing to do with cellular localization.",
    "401547": "Hi Francisco, thanks for your feedback!\n\n&gt; To the organisers: Were the images captured using the same instrument, or if not, using the same settings? More importantly, is signal intensity uniform (and therefore comparable) across all images?\n\nThe images were not captured on the same instrument, although we've used the same instrument model for all images. Most settings are the same but not all, and particularly not laser and detector settings. So I don't think that signal intensity is comparable across all images.",
    "402745": "Thank you, that answers my question!",
    "402749": "Hi Tilii. Yes, the fact that different cell types are used complicates things, and I agree it might be that they do not express proteins equally well. As for cells that have grown longer having stronger signal, I disagree in the sense that the light irradiating the cells focuses on focal planes. Here is an example using a pollen grain.\n![https://www.olympus-lifescience.com][1]\n\nHowever, I have seen some images that barely show anything in green, and in those situations intensity normalisation is bound to increase noise.\n\n\n  [1]: https://static1.olympus-lifescience.com/data/olympusmicro/primer/techniques/confocal/images/confocalintrofigure6.jpg?rev=E606"
  },
  "source": "meta"
}