Comments (4)
I started this a while ago but the SpaceTx/Starfish objects are not as nice as AnnData. We need this anyway for HuBMAP
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Yeah the proprietary image data structures look like they may be tricky to work with. It looks like there are some conversion functions, (maybe you have already seen them):
- https://spacetx-starfish.readthedocs.io/en/latest/api/data_structures/image_stack.html#starfish.core.imagestack.imagestack.ImageStack.to_multipage_tiff
- https://spacetx-starfish.readthedocs.io/en/latest/api/data_structures/expression_matrix.html#starfish.core.expression_matrix.expression_matrix.ExpressionMatrix.save_anndata
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Yes I had seen that - I think my biggest hurdle was the fact that there isn't one object always returned. There are many possible "end results" so I sort of stopped, faced with the options, at the point of writing a wrapper since it was not clear to me what should be wrapped - anything returned or certain objects? And then there are non-returned results like the tiff which is an input but you want to visualize it. I imagine I was overthinking it but I became overwhelmed as happens sometimes....
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Ah I see. Maybe when it is ambiguous about what to visualize, special parameters (like we have for AnnDataWrapper https://github.com/vitessce/vitessce-python/blob/44bb572/vitessce/wrappers.py#L319) could help?
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Related Issues (20)
- Minimal example for obsSegmentations.json for visualizing polygons in Spatial View HOT 2
- Adding scale bar to spatial view image
- ValueError: data too large for non-BigTIFF file HOT 4
- Additional improvements to adata_to_multivec_zarr function
- Add option for widget to communicate directly with Zarr store (no local HTTP server) HOT 2
- Bumping supported Anndata Version? HOT 1
- Support automatic instantiation of Wrapper objects HOT 2
- Support using JSX for writing plugin views
- Setting colors for obsSets? HOT 2
- Helper function to use adata.uns[obs_set_col + "_colors"] for initial obs set colors
- Notebooks environment.yml PackageNotFoundError for starlette==0.14.0
- Notebooks errors (list)
- Adding Vitessce widgets to a visualization dashboard HOT 1
- Define a plugin class/dataclass to couple on_config_change and anywidget.invoke handlers with plugin_esm HOT 1
- Support writing plugin_esm using local file with anywidget FileContents
- Ability to use comparative views + pageMode in a Jupyter notebook
- Warn if AnnDataWrapper options are empty as it would result in empty list for `vc['datasets']['files']` HOT 4
- Vitessce python on remote jupyter servers do not work HOT 3
- Command functions should be able to return an updated config HOT 1
- Enable `numpy` v2 Support/Unpin `numpy` v1
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