{
  "id": 553189,
  "title": "Visualization training zarr data by itkwidgets in Colab (cannot Kaggle notebook)",
  "url": "/competitions/czii-cryo-et-object-identification/discussion/553189",
  "author_name": "kebenny",
  "post_date": "2024-12-24T08:21:41.167000",
  "votes": 4,
  "comment_count": 0,
  "views": 0,
  "content": "<p>Copy a zarr folder to Colab. Few lines of code can visualize training zarr data by itkwidgets.</p>\n<p><code>pip install -q 'itkwidgets[all]&gt;=1.0a49'</code><br>\n<code>pip install zarr</code><br>\n<code>import zarr</code><br>\n<code>from itkwidgets import view</code><br>\n<code>czii_zarr_path = '/content/drive/MyDrive/denoised_TS_5_4.zarr'</code><br>\n<code>zarr_file = zarr.open(czii_zarr_path, mode='r')</code><br>\n<code>view(zarr_file)</code></p>\n<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F12088692%2Ff4dc8853ba7720d9b1bfb333bea3d14d%2F20241224.png?generation=1735028350562758&amp;alt=media\" alt=\"\"></p>\n<p>I tried to run in Kaggle but following error occurs.<br>\nRuntimeError: itkwidgets 1.0a51 and newer requires Jupyter notebook&gt;=7.</p>",
  "messages": [
    {
      "id": 3079850,
      "postDate": "2024-12-24T08:21:41.167Z",
      "content": "<p>Copy a zarr folder to Colab. Few lines of code can visualize training zarr data by itkwidgets.</p>\n<p><code>pip install -q 'itkwidgets[all]&gt;=1.0a49'</code><br>\n<code>pip install zarr</code><br>\n<code>import zarr</code><br>\n<code>from itkwidgets import view</code><br>\n<code>czii_zarr_path = '/content/drive/MyDrive/denoised_TS_5_4.zarr'</code><br>\n<code>zarr_file = zarr.open(czii_zarr_path, mode='r')</code><br>\n<code>view(zarr_file)</code></p>\n<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F12088692%2Ff4dc8853ba7720d9b1bfb333bea3d14d%2F20241224.png?generation=1735028350562758&amp;alt=media\" alt=\"\"></p>\n<p>I tried to run in Kaggle but following error occurs.<br>\nRuntimeError: itkwidgets 1.0a51 and newer requires Jupyter notebook&gt;=7.</p>",
      "rawMarkdown": "Copy a zarr folder to Colab. Few lines of code can visualize training zarr data by itkwidgets.\n\n`pip install -q 'itkwidgets[all]>=1.0a49'`\n`pip install zarr`\n`import zarr`\n`from itkwidgets import view`\n`czii_zarr_path = '/content/drive/MyDrive/denoised_TS_5_4.zarr'`\n`zarr_file = zarr.open(czii_zarr_path, mode='r')`\n`view(zarr_file)`\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F12088692%2Ff4dc8853ba7720d9b1bfb333bea3d14d%2F20241224.png?generation=1735028350562758&alt=media)\n\nI tried to run in Kaggle but following error occurs.\nRuntimeError: itkwidgets 1.0a51 and newer requires Jupyter notebook>=7.",
      "votes": 4
    }
  ],
  "comments": [],
  "raw_markdown_by_id": {
    "3079850": "Copy a zarr folder to Colab. Few lines of code can visualize training zarr data by itkwidgets.\n\n`pip install -q 'itkwidgets[all]>=1.0a49'`\n`pip install zarr`\n`import zarr`\n`from itkwidgets import view`\n`czii_zarr_path = '/content/drive/MyDrive/denoised_TS_5_4.zarr'`\n`zarr_file = zarr.open(czii_zarr_path, mode='r')`\n`view(zarr_file)`\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F12088692%2Ff4dc8853ba7720d9b1bfb333bea3d14d%2F20241224.png?generation=1735028350562758&alt=media)\n\nI tried to run in Kaggle but following error occurs.\nRuntimeError: itkwidgets 1.0a51 and newer requires Jupyter notebook>=7."
  }
}