{
  "id": 164934,
  "title": "Pydicom Image Preprocessing Discussion",
  "url": "/competitions/osic-pulmonary-fibrosis-progression/discussion/164934",
  "author_name": "",
  "post_date": "2020-07-07T23:20:32.455887600Z",
  "votes": 3,
  "comment_count": 7,
  "views": 0,
  "content": "<p>Please share best practice and experience about Pydicom image preprocessing </p>\n\n<ol>\n<li>Image Preprocessing</li>\n<li>Image information Extraction</li>\n<li>Image Augmentation</li>\n<li>Using Meta data</li>\n</ol>",
  "messages": [
    {
      "id": "919503",
      "postDate": "07/07/2020 23:20:32",
      "content": "<p>Please share best practice and experience about Pydicom image preprocessing </p>\n\n<ol>\n<li>Image Preprocessing</li>\n<li>Image information Extraction</li>\n<li>Image Augmentation</li>\n<li>Using Meta data</li>\n</ol>",
      "rawMarkdown": "Please share best practice and experience about Pydicom image preprocessing \n\n1. Image Preprocessing\n2. Image information Extraction\n3. Image Augmentation\n4. Using Meta data",
      "votes": null
    },
    {
      "id": "919505",
      "postDate": "07/07/2020 23:21:27",
      "content": "<p>Kevin Mader, Lung Opacity Overview, <a href=\"https://www.kaggle.com/kmader/lung-opacity-overview\">https://www.kaggle.com/kmader/lung-opacity-overview</a>\nModality Specific Modules, DICOM Standard, <a href=\"http://dicom.nema.org/medical/dicom/2014c/output/chtml/part03/sect_C.8.html\">http://dicom.nema.org/medical/dicom/2014c/output/chtml/part03/sect_C.8.html</a>\nDICOM Standard, <a href=\"https://www.dicomstandard.org/\">https://www.dicomstandard.org/</a>\nGetting Started with Pydicom, <a href=\"https://pydicom.github.io/pydicom/stable/getting_started.html\">https://pydicom.github.io/pydicom/stable/getting_started.html</a>\nITKPYthon package, <a href=\"https://itkpythonpackage.readthedocs.io/en/latest/\">https://itkpythonpackage.readthedocs.io/en/latest/</a>\nDICOM in Python: Importing medical image data into NumPy with PyDICOM and VTK, * * * <a href=\"https://pyscience.wordpress.com/2014/09/08/dicom-in-python-importing-medical-image-data-into-numpy-with-pydicom-and-vtk/\">https://pyscience.wordpress.com/2014/09/08/dicom-in-python-importing-medical-image-data-into-numpy-with-pydicom-and-vtk/</a>\nDICOM Processing and Segmentation in Python, <a href=\"https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/\">https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/</a>\nDICOM Standard Browser, <a href=\"https://dicom.innolitics.com/ciods\">https://dicom.innolitics.com/ciods</a>\nHow can I read a DICOM image in Python, <a href=\"https://www.quora.com/How-can-I-read-a-DICOM-image-in-Python\">https://www.quora.com/How-can-I-read-a-DICOM-image-in-Python</a>\nDICOM read example in Python, <a href=\"https://www.programcreek.com/python/example/97517/dicom.read_file\">https://www.programcreek.com/python/example/97517/dicom.read_file</a>\nDICOM in Python, <a href=\"https://github.com/pydicom\">https://github.com/pydicom</a>\nAny other useful information, Please share here.</p>",
      "rawMarkdown": "Kevin Mader, Lung Opacity Overview, https://www.kaggle.com/kmader/lung-opacity-overview\nModality Specific Modules, DICOM Standard, http://dicom.nema.org/medical/dicom/2014c/output/chtml/part03/sect_C.8.html\nDICOM Standard, https://www.dicomstandard.org/\nGetting Started with Pydicom, https://pydicom.github.io/pydicom/stable/getting_started.html\nITKPYthon package, https://itkpythonpackage.readthedocs.io/en/latest/\nDICOM in Python: Importing medical image data into NumPy with PyDICOM and VTK, * * * https://pyscience.wordpress.com/2014/09/08/dicom-in-python-importing-medical-image-data-into-numpy-with-pydicom-and-vtk/\nDICOM Processing and Segmentation in Python, https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/\nDICOM Standard Browser, https://dicom.innolitics.com/ciods\nHow can I read a DICOM image in Python, https://www.quora.com/How-can-I-read-a-DICOM-image-in-Python\nDICOM read example in Python, https://www.programcreek.com/python/example/97517/dicom.read_file\nDICOM in Python, https://github.com/pydicom\nAny other useful information, Please share here.",
      "votes": null
    },
    {
      "id": "920321",
      "postDate": "07/08/2020 13:57:44",
      "content": "<p>Medium article showing example of processing and analyzing chest CT scans using pydicom: <a href=\"https://medium.com/&lt;a href=\">@hengloose</a>/a-comprehensive-starter-guide-to-visualizing-and-analyzing-dicom-images-in-python-7a8430fcb7ed\"&gt;https://medium.com/<a href=\"/hengloose\">@hengloose</a>/a-comprehensive-starter-guide-to-visualizing-and-analyzing-dicom-images-in-python-7a8430fcb7ed </p>",
      "rawMarkdown": "Medium article showing example of processing and analyzing chest CT scans using pydicom: https://medium.com/@hengloose/a-comprehensive-starter-guide-to-visualizing-and-analyzing-dicom-images-in-python-7a8430fcb7ed",
      "votes": null
    },
    {
      "id": "950050",
      "postDate": "07/29/2020 06:31:11",
      "content": "<p>Thanks <a href=\"/arachauhan\">@arachauhan</a> for the links. This link in particular is very helpful: <a href=\"https://www.kaggle.com/kmader/lung-opacity-overview\">https://www.kaggle.com/kmader/lung-opacity-overview</a> (Kevin Mader, Lung Opacity Overview)</p>",
      "rawMarkdown": "Thanks @arachauhan for the links. This link in particular is very helpful: https://www.kaggle.com/kmader/lung-opacity-overview (Kevin Mader, Lung Opacity Overview)",
      "votes": null
    },
    {
      "id": "959070",
      "postDate": "08/05/2020 10:08:41",
      "content": "<p>one more by fastai\n<a href=\"https://towardsdatascience.com/understanding-dicoms-835cd2e57d0b\">towardsdatascience.com/understanding-dicoms</a></p>\n\n<p>and an article (I.J. Radiology and Imaging)\n<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354356/\">Managing DICOM images: Tips and tricks for the radiologist</a></p>",
      "rawMarkdown": "one more by fastai\n[towardsdatascience.com/understanding-dicoms](https://towardsdatascience.com/understanding-dicoms-835cd2e57d0b)\n\nand an article (I.J. Radiology and Imaging)\n[Managing DICOM images: Tips and tricks for the radiologist](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354356/)",
      "votes": null
    },
    {
      "id": "962314",
      "postDate": "08/08/2020 03:30:22",
      "content": "<p><a href=\"http://uwmsk.org/jupyter/Jupyter_DICOM_toolbox.html\">http://uwmsk.org/jupyter/Jupyter_DICOM_toolbox.html</a></p>\n\n<p>I found this really helpful especially to deal with dark images.</p>",
      "rawMarkdown": "http://uwmsk.org/jupyter/Jupyter_DICOM_toolbox.html\n\nI found this really helpful especially to deal with dark images.",
      "votes": null
    },
    {
      "id": "974821",
      "postDate": "08/18/2020 04:13:25",
      "content": "<p>came across the original version of this here with explanations:<br>\n<a href=\"https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/\" target=\"_blank\">https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/</a></p>",
      "rawMarkdown": "came across the original version of this here with explanations:\nhttps://www.raddq.com/dicom-processing-segmentation-visualization-in-python/",
      "votes": null
    },
    {
      "id": "975535",
      "postDate": "08/18/2020 10:45:37",
      "content": "<p>FAST.AI has excellent library dedicated for medical imaging.<br>\ncheck it out here  <a href=\"https://dev.fast.ai/medical.imaging\" target=\"_blank\">https://dev.fast.ai/medical.imaging</a></p>",
      "rawMarkdown": "FAST.AI has excellent library dedicated for medical imaging.\ncheck it out here  https://dev.fast.ai/medical.imaging",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 975535,
      "author_name": "rajnishe",
      "author_url": "",
      "post_date": "08/18/2020 10:45:37",
      "content": "<p>FAST.AI has excellent library dedicated for medical imaging.<br>\ncheck it out here  <a href=\"https://dev.fast.ai/medical.imaging\" target=\"_blank\">https://dev.fast.ai/medical.imaging</a></p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 919505,
      "author_name": "arachauhan",
      "author_url": "",
      "post_date": "07/07/2020 23:21:27",
      "content": "<p>Kevin Mader, Lung Opacity Overview, <a href=\"https://www.kaggle.com/kmader/lung-opacity-overview\">https://www.kaggle.com/kmader/lung-opacity-overview</a>\nModality Specific Modules, DICOM Standard, <a href=\"http://dicom.nema.org/medical/dicom/2014c/output/chtml/part03/sect_C.8.html\">http://dicom.nema.org/medical/dicom/2014c/output/chtml/part03/sect_C.8.html</a>\nDICOM Standard, <a href=\"https://www.dicomstandard.org/\">https://www.dicomstandard.org/</a>\nGetting Started with Pydicom, <a href=\"https://pydicom.github.io/pydicom/stable/getting_started.html\">https://pydicom.github.io/pydicom/stable/getting_started.html</a>\nITKPYthon package, <a href=\"https://itkpythonpackage.readthedocs.io/en/latest/\">https://itkpythonpackage.readthedocs.io/en/latest/</a>\nDICOM in Python: Importing medical image data into NumPy with PyDICOM and VTK, * * * <a href=\"https://pyscience.wordpress.com/2014/09/08/dicom-in-python-importing-medical-image-data-into-numpy-with-pydicom-and-vtk/\">https://pyscience.wordpress.com/2014/09/08/dicom-in-python-importing-medical-image-data-into-numpy-with-pydicom-and-vtk/</a>\nDICOM Processing and Segmentation in Python, <a href=\"https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/\">https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/</a>\nDICOM Standard Browser, <a href=\"https://dicom.innolitics.com/ciods\">https://dicom.innolitics.com/ciods</a>\nHow can I read a DICOM image in Python, <a href=\"https://www.quora.com/How-can-I-read-a-DICOM-image-in-Python\">https://www.quora.com/How-can-I-read-a-DICOM-image-in-Python</a>\nDICOM read example in Python, <a href=\"https://www.programcreek.com/python/example/97517/dicom.read_file\">https://www.programcreek.com/python/example/97517/dicom.read_file</a>\nDICOM in Python, <a href=\"https://github.com/pydicom\">https://github.com/pydicom</a>\nAny other useful information, Please share here.</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 920321,
      "author_name": "gleas17",
      "author_url": "",
      "post_date": "07/08/2020 13:57:44",
      "content": "<p>Medium article showing example of processing and analyzing chest CT scans using pydicom: <a href=\"https://medium.com/&lt;a href=\">@hengloose</a>/a-comprehensive-starter-guide-to-visualizing-and-analyzing-dicom-images-in-python-7a8430fcb7ed\"&gt;https://medium.com/<a href=\"/hengloose\">@hengloose</a>/a-comprehensive-starter-guide-to-visualizing-and-analyzing-dicom-images-in-python-7a8430fcb7ed </p>",
      "votes": null,
      "replies": [
        {
          "id": 974821,
          "author_name": "hanhmpham",
          "author_url": "",
          "post_date": "08/18/2020 04:13:25",
          "content": "<p>came across the original version of this here with explanations:<br>\n<a href=\"https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/\" target=\"_blank\">https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/</a></p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 950050,
      "author_name": "yixiang",
      "author_url": "",
      "post_date": "07/29/2020 06:31:11",
      "content": "<p>Thanks <a href=\"/arachauhan\">@arachauhan</a> for the links. This link in particular is very helpful: <a href=\"https://www.kaggle.com/kmader/lung-opacity-overview\">https://www.kaggle.com/kmader/lung-opacity-overview</a> (Kevin Mader, Lung Opacity Overview)</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 959070,
      "author_name": "imeintanis",
      "author_url": "",
      "post_date": "08/05/2020 10:08:41",
      "content": "<p>one more by fastai\n<a href=\"https://towardsdatascience.com/understanding-dicoms-835cd2e57d0b\">towardsdatascience.com/understanding-dicoms</a></p>\n\n<p>and an article (I.J. Radiology and Imaging)\n<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354356/\">Managing DICOM images: Tips and tricks for the radiologist</a></p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 962314,
      "author_name": "havinath",
      "author_url": "",
      "post_date": "08/08/2020 03:30:22",
      "content": "<p><a href=\"http://uwmsk.org/jupyter/Jupyter_DICOM_toolbox.html\">http://uwmsk.org/jupyter/Jupyter_DICOM_toolbox.html</a></p>\n\n<p>I found this really helpful especially to deal with dark images.</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "919503": "Please share best practice and experience about Pydicom image preprocessing \n\n1. Image Preprocessing\n2. Image information Extraction\n3. Image Augmentation\n4. Using Meta data",
    "919505": "Kevin Mader, Lung Opacity Overview, https://www.kaggle.com/kmader/lung-opacity-overview\nModality Specific Modules, DICOM Standard, http://dicom.nema.org/medical/dicom/2014c/output/chtml/part03/sect_C.8.html\nDICOM Standard, https://www.dicomstandard.org/\nGetting Started with Pydicom, https://pydicom.github.io/pydicom/stable/getting_started.html\nITKPYthon package, https://itkpythonpackage.readthedocs.io/en/latest/\nDICOM in Python: Importing medical image data into NumPy with PyDICOM and VTK, * * * https://pyscience.wordpress.com/2014/09/08/dicom-in-python-importing-medical-image-data-into-numpy-with-pydicom-and-vtk/\nDICOM Processing and Segmentation in Python, https://www.raddq.com/dicom-processing-segmentation-visualization-in-python/\nDICOM Standard Browser, https://dicom.innolitics.com/ciods\nHow can I read a DICOM image in Python, https://www.quora.com/How-can-I-read-a-DICOM-image-in-Python\nDICOM read example in Python, https://www.programcreek.com/python/example/97517/dicom.read_file\nDICOM in Python, https://github.com/pydicom\nAny other useful information, Please share here.",
    "920321": "Medium article showing example of processing and analyzing chest CT scans using pydicom: https://medium.com/@hengloose/a-comprehensive-starter-guide-to-visualizing-and-analyzing-dicom-images-in-python-7a8430fcb7ed",
    "950050": "Thanks @arachauhan for the links. This link in particular is very helpful: https://www.kaggle.com/kmader/lung-opacity-overview (Kevin Mader, Lung Opacity Overview)",
    "959070": "one more by fastai\n[towardsdatascience.com/understanding-dicoms](https://towardsdatascience.com/understanding-dicoms-835cd2e57d0b)\n\nand an article (I.J. Radiology and Imaging)\n[Managing DICOM images: Tips and tricks for the radiologist](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354356/)",
    "962314": "http://uwmsk.org/jupyter/Jupyter_DICOM_toolbox.html\n\nI found this really helpful especially to deal with dark images.",
    "974821": "came across the original version of this here with explanations:\nhttps://www.raddq.com/dicom-processing-segmentation-visualization-in-python/",
    "975535": "FAST.AI has excellent library dedicated for medical imaging.\ncheck it out here  https://dev.fast.ai/medical.imaging"
  },
  "source": "meta"
}