navinlabcode / navinlabcode/CellTrek

Visualization and error in celltrek_vis

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Dominant language
R
Stars
135
Forks
23
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Description

Hi,

Congratulations on such a great tool! I am hoping you can help me figure out the following issues I've encountered:

  1. In celltrek_vis, I get the following error in the Shiny app pop-up: "
    Error: no applicable method for 'as.raster' applied to an object of class "c('VisiumV1', 'SpatialImage')"
  2. Without celltrek_vis working, I visualized the cells on the Visium embedding as follows:
    DimPlot(brain_celltrek, reduction='celltrek_raw', group.by = "CellType")
    But this doesn't give me the H&E image. Do you have any suggestions on how to get this to work? Or No. 1 above? I think either one will help solve the issue.
  3. Lastly, when calculating the spatial weighted cross-correlation, I noticed that the CC scores are too big and are not positioned correctly to the HE image. Do you have any suggestions on how to resolve this?

Thank you very much for your help!

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  1. Read the whole issue, then the project's contributing guide.
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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the celltrek_vis entry point and reproduce the Shiny error involving as.raster on the VisiumV1 SpatialImage object. Then inspect the visualization path for the H&E image and the spatial weighted cross-correlation inputs, using the reported image-position and score-size discrepancies as checks. Done means the popup renders the image and the plotted cells and correlation scores align with the H&E image.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data-visualization
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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