Efficiently storing millions of spots
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- Dominant language
- Python
- Stars
- 171
- Forks
- 75
- Avg merge
- 2d 3h
- Merged PRs (30d)
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Description
@d-v-b following up on our discussion in zoom just right now: would you have a recommendation for how to store the output of a spatial-omics analysis, i.e. millions of spots, where a spot has one (or in our case several) 2D or 3D coordinates, a gene name string, and maybe some additional properties such as "detection quality". I think requirements would be column-wise (and row-wise) chunked loading from a file system but also from "the internet" (maybe S3 object store).
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with issue #178 and read its 17-comment discussion, focusing on the stated requirements for millions of spatial-omics spots, multidimensional coordinates, properties, chunked access, and object storage. Done would require a decided storage recommendation or specification direction; no files or tests are named in the issue.
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Assessment
- Tech stack
- aws
- Domain
- bioinformatics, cloud, data-engineering
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100