Description
We need to document how to use the notebook 00_core_selection_demo.ipynb. This section should guide a new user through the process of detecting and saving cores using the SAM2 model in combination with napari.
The documentation should include:
- An explanation of the role of the “cores” and “bounding boxes” layers in napari
- A difference between using square and polygon ROIs.
- Link to napari resources describing shapes layer and its tools.
- A step-by-step description of how to use the SAM2 model to generate initial suggestions for core localization
- Instructions for saving the detected cores after selection (files to be expected)
In addition, create a short video tutorial that demonstrates the workflow (assuming SAM2 is already set up). The video should show only the interaction with the notebook and napari.
Done when
Optional feedback
While working on this task, if you notice opportunities to improve the user-friendliness of this step (e.g., napari buttons layout, workflow, etc.), please add a comment in this issue.
This is not required to close the issue — the main deliverables are listed in Acceptance criteria.
Description
We need to document how to use the notebook
00_core_selection_demo.ipynb. This section should guide a new user through the process of detecting and saving cores using the SAM2 model in combination with napari.The documentation should include:
In addition, create a short video tutorial that demonstrates the workflow (assuming SAM2 is already set up). The video should show only the interaction with the notebook and napari.
Done when
Optional feedback
While working on this task, if you notice opportunities to improve the user-friendliness of this step (e.g., napari buttons layout, workflow, etc.), please add a comment in this issue.
This is not required to close the issue — the main deliverables are listed in Acceptance criteria.