Skip to content

Update Colab demo notebook #128

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
C-Achard merged 11 commits into from
May 22, 2026
Merged

Update Colab demo notebook #128

Changes from 2 commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
4244ebe
Fix URL
C-Achard May 21, 2026
062f994
Add uv install
C-Achard May 21, 2026
949d0d0
Add force restart after install
C-Achard May 21, 2026
e325c4e
Add better checks for install
C-Achard May 21, 2026
c84d6ee
Fix URL again
C-Achard May 21, 2026
f0653cc
Fix commands syntax
C-Achard May 21, 2026
265e0a1
Update Colab_inference_demo.ipynb
C-Achard May 21, 2026
5be31ff
Update Colab_inference_demo.ipynb
C-Achard May 21, 2026
b3d6cac
Colab demo: ensure demo data; refine install flow
C-Achard May 21, 2026
eb8c292
URL case fix
C-Achard May 21, 2026
8a32c37
Update test_plugins.py
C-Achard May 21, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 10 additions & 2 deletions notebooks/Colab_inference_demo.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
"id": "view-in-github"
},
"source": [
"<a href=\"https://colab.research.google.com/github/MMathisLab/CellSeg3d/blob/main/Notebooks/Colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
"<a href=\"https://colab.research.google.com/github/AdaptiveMotorControlLab/CellSeg3d/blob/main/Notebooks/Colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
Comment thread
C-Achard marked this conversation as resolved.
Outdated
]
},
{
Expand Down Expand Up @@ -54,8 +54,16 @@
"outputs": [],
"source": [
"# @markdown ##Install CellSeg3D and grab demo data\n",
"!curl -LsSf https://astral.sh/uv/install.sh | sh\n",
"import os\n",
Comment thread
C-Achard marked this conversation as resolved.
Outdated
"\n",
"os.environ[\"PATH\"] += \":/root/.local/bin\"\n",
Comment thread
C-Achard marked this conversation as resolved.
Outdated
"\n",
"# Clone CellSeg3D\n",
"!git clone https://github.com/AdaptiveMotorControlLab/CellSeg3d.git --branch main --single-branch ./CellSeg3D\n",
"!pip install napari-cellseg3d"
"\n",
"# Install with uv\n",
"!uv pip install napari-cellseg3d"
]
},
{
Expand Down
Loading