[add] Baysor Scaling factor
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 46
- Forks
- 23
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
Baysor scale param corresponds to the cell radius and not the diameter
Using --scale 30 on Xenium data with an expected cell radius of 30 µm (60 µm diameter) results in under-segmentation across many tissue types. This needs to change with a standard table where users can select the scale factor based on the cells they are looking at.
If the scale factor is too large (eg. current value - 30) this results in undersegmented cells due to cell merging
if the scale factor is low this would result in over-segmented cells.
We need to come up with a reference table in the README
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
Start by reviewing the README and the existing Baysor scale guidance. Define a reference table that relates cell radius and diameter to suitable scale factors, including the under-segmentation and over-segmentation risks described in the issue. Done means the README clearly lets users select an appropriate scale for their cell type.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100