scverse / scverse/napari-spatialdata
make multicolor images
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- Dominant language
- Python
- Stars
- 90
- Forks
- 25
- Avg merge
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- Merged PRs (30d)
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Description
Thanks for all your work on spatialdata and napari viewer.
Unless i have missed it, one missing aspect i would like is the ability to make multicolor images of image elemtns in spatialdata objects, within the spatial-data napari viewer plugin. So far as i can tell, this is not possible.
Expected behaviour
- Load spatial data in napari with spatialdata plugin
- Select coordinate system, load image element
- Select a channel, adjust colormap and contrast limits
- Select another channel, repeat step 3 until showing all channels as one would like
- Have multichannel view of image, on which can overlay mask elements
Issue
Selecting a second channel, resets the whole image. Can only view one image at a time
Potential solutions
Option to load channels as individual image layers?
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.
Research direction
Reproduce the issue in the napari spatialdata plugin using the five-step workflow described: load an image element, adjust one channel, then select another. Trace how channel selection resets the image, and confirm the existing behavior for overlaying mask elements. Done means multiple selected channels remain visible together with independent colormaps and contrast limits, while mask overlays still work.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100