Add quickstart for the VCP #343
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edyoshikun
requested review from
KRCora,
alxndrkalinin,
mattersoflight and
srivarra
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
| # %% | ||
| # Validate installation | ||
| # !viscy --help | ||
|
|
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Suggested change
| ### Download example data and model checkpoint | |
| Estimated download time: XX |
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@edyoshikun FYI this step is taking a long time... I wasn't able to run it on Colab's free tier (ran out of disk space). Trying on Colab Enterprise
KRCora
reviewed
Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
KRCora
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Nov 26, 2025
KRCora
reviewed
Nov 26, 2025
melissawm
reviewed
Nov 27, 2025
Comment on lines
83
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| "\"\"\"\n", | ||
| "Setup\n", | ||
| "\n", | ||
| "The commands below will install the required packages and download the example dataset and model checkpoint.\n", | ||
| "\n", | ||
| "Setup notes:\n", | ||
| "\n", | ||
| "- **Setting up Google Colab**: To run this quickstart guide using Google Colab, choose the 'T4' GPU runtime from the \"Connect\" dropdown menu in the upper-right corner of this notebook for faster execution.\n", | ||
| "Using a GPU significantly speeds up running model inference, but CPU compute can also be used.\n", | ||
| "\n", | ||
| "- **Setting up local environment**: The commands below assume a Unix-like shell with `wget` installed. On Windows, the files can be downloaded manually from the URLs.\n", | ||
| "On Windows, the files can be downloaded manually from the URLs.\n", | ||
| "\n", | ||
| "\"\"\"\n", |
Contributor
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I think something's wrong with the formatting here (looking at the rendered notebook shows extra quotes):
Suggested change
| "\"\"\"\n", | |
| "Setup\n", | |
| "\n", | |
| "The commands below will install the required packages and download the example dataset and model checkpoint.\n", | |
| "\n", | |
| "Setup notes:\n", | |
| "\n", | |
| "- **Setting up Google Colab**: To run this quickstart guide using Google Colab, choose the 'T4' GPU runtime from the \"Connect\" dropdown menu in the upper-right corner of this notebook for faster execution.\n", | |
| "Using a GPU significantly speeds up running model inference, but CPU compute can also be used.\n", | |
| "\n", | |
| "- **Setting up local environment**: The commands below assume a Unix-like shell with `wget` installed. On Windows, the files can be downloaded manually from the URLs.\n", | |
| "On Windows, the files can be downloaded manually from the URLs.\n", | |
| "\n", | |
| "\"\"\"\n", | |
| "### Setup\n", | |
| "\n", | |
| "The commands below will install the required packages and download the example dataset and model checkpoint.\n", | |
| "\n", | |
| "Setup notes:\n", | |
| "\n", | |
| "- **Setting up Google Colab**: To run this quickstart guide using Google Colab, choose the 'T4' GPU runtime from the \"Connect\" dropdown menu in the upper-right corner of this notebook for faster execution.\n", | |
| "Using a GPU significantly speeds up running model inference, but CPU compute can also be used.\n", | |
| "\n", | |
| "- **Setting up local environment**: The commands below assume a Unix-like shell with `wget` installed. On Windows, the files can be downloaded manually from the URLs.\n", | |
| "On Windows, the files can be downloaded manually from the URLs.\n", |
melissawm
reviewed
Nov 27, 2025
| "cell_marker": "\"\"\"" | ||
| }, | ||
| "source": [ | ||
| "# Prerequisites\n", |
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Suggested change
| "# Prerequisites\n", | |
| "## Prerequisites\n", |
melissawm
reviewed
Nov 27, 2025
| "axes[1].set_ylabel(\"PHATE 2\")\n", | ||
| "\n", | ||
| "plt.tight_layout()\n", | ||
| "plt.show()" |
Contributor
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This cell does not work for me, due to an issue with not finding the extracted_inf_state.csv file.
FileNotFoundError: [Errno 2] No such file or directory: 'extracted_inf_state.csv'
Did we fail to download this file in an earlier step?
Member
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I figured out the bug. 1) I forgot to write the wget for downloading 2) the permission for the file were set to 750. Thanks!
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ab92b74 the notebook now reflects the download of this data and the csv file needed to run the rest of the exercise
Contributor
|
Hi @edyoshikun - thanks for this! Last comments:
After installing phate, the notebook runs great 🎉 |
melissawm
approved these changes
Dec 1, 2025
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Looks great! When you merge this, we can use add the notebook URL to the VCP so it's linked from there. Thank you!
srivarra
approved these changes
Dec 1, 2025
KRCora
reviewed
Dec 2, 2025
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This PR adds a quickstart demo for the VCP