Notebook on 3D data and on images from multiple imaging cycles
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Documentation
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- jupyter-notebook, numpy
Research direction
Review the new transformations refactoring and the merged stitch notebook first. Build a notebook covering 2D slices or max projections from large 3D images, stacking images from multiple cycles with rotation, re-rasterization, and cropping, and visualizing 2D layers in 3D with napari. Done means both related workflows are demonstrated together.
Written by the indexing model from the issue text.
Description
Two related concepts that would be nice to show, and show in the same notebook (from a discussion with @lopollar and @melonora).
Sometimes the user has a large 3D image and wants to operate on a 2D slice (or use a 2D max projection), and sometime the users have many two images and want to stack them together in a 3D image, or in a 2D multichannel image (the stacking is not just a "numpy array stacking", but it could involve rotations, etc and requires re-rasterization and cropping).
After the new transformations refactoring and the merge of the stitch notebook this will be supported and it would be nice to show this to the user, together with a napari viz of the 2D layers embedded in the 3D space.
- Dominant language
- Jupyter Notebook
- Stars
- 67
- Forks
- 26
- Avg merge
- 4m
- Merged PRs (30d)
- 1
Contributor guide
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