Reproduce Napari visualizations
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 30/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- python
- Domain
- data-visualization
Research direction
Start by reviewing the existing spatialdata-plot rendering path and the NGFF Omero metadata described in the issue. Determine how visualization presets are currently read, then define acceptance checks for additive or opaque blending, Napari-style colors, and absolute contrast limits or windows. Done means static previews reproduce the requested preset properties without opening Napari interactively.
Written by the indexing model from the issue text.
Description
I would like to generate static images files from NGFF/SpatialData datasets and presets stored in their NGFF Omero metadata, so that one can preview datasets without opening them interactively in Napari.
This combines the idea that SpatialData's data model resembles Napari's, and that datasets can store visualization presets for a reasonable default visualization.
For this, we still need some basic rendering properties:
blending:additive|opaque…
Typically, images contain multiple channel, and their visualization is different depending on the microscopy illumination type. Several fluorescence channels can be visualized in a single image by additive blending. However, currently spatialdata-plot "overwrites" pixels of channels underneath.color:
Napari allows to provide a color name for maximum intensity values and generates a corresponding color map.contrast_limits(Napari) orwindow(Omero):
Typically, the value range of images can differ greatly, and in order to avoid reading all pixels to compute limits, Omero stores absolute limits in the metadata. However, spatialdata-plot currently supports only Matplotlib's relative limitspmin/pmax(asquantiles_for_norm).
- Dominant language
- Python
- Stars
- 86
- Forks
- 21
- Avg merge
- 14h 50m
- Merged PRs (30d)
- 3
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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