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https://github.com/keller-mark/visium-dlpfc-processing
https://github.com/keller-mark/visium-dlpfc-processing
Last synced: 12 days ago
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- Host: GitHub
- URL: https://github.com/keller-mark/visium-dlpfc-processing
- Owner: keller-mark
- Created: 2024-02-29T18:12:52.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2024-03-04T18:07:33.000Z (11 months ago)
- Last Synced: 2024-11-13T06:21:50.714Z (2 months ago)
- Language: Jupyter Notebook
- Size: 430 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# visium-dlpfc
Sample 151673
Data obtained from:
- RData file: https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1 (linked from https://github.com/LieberInstitute/spatialLIBD/blob/ff49a2eaa1eb5477c5df8e46cf1652cdd8ec7244/R/fetch_data.R#L142C18-L142C125)
- Manual layer annotations: https://drive.google.com/drive/folders/10lhz5VY7YfvHrtV40MwaqLmWz56U9eBP?usp=sharing (linked from https://stagate.readthedocs.io/en/latest/T1_DLPFC.html)
- TIFF image: https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151673_full_image.tif (linked from https://github.com/LieberInstitute/spatialLIBD/blob/ff49a2eaa1eb5477c5df8e46cf1652cdd8ec7244/README.md?plain=1#L235)
Data conversion
## RData to rds
```R
load("Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata")
saveRDS(sce, file="Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.rds")
```
## rds to AnnData with manual layer annotations
See Jupyter notebook `convert_rds_to_adata.ipynb`
## All to SpatialData
See Jupyter notebook `convert_all_to_spatialdata.ipynb`
## To obtain scale factors
```R
> library(STexampleData)
> spe <- Visium_humanDLPFC()
> imgData(spe)
DataFrame with 2 rows and 4 columns
sample_id image_id data scaleFactor
1 sample_151673 lowres #### 0.0450045
2 sample_151673 hires #### 0.1500150
> imgData(spe)[1, 'data']
[[1]]
600 x 600 (width x height) LoadedSpatialImage
> imgData(spe)[2, 'data']
[[1]]
2000 x 2000 (width x height) LoadedSpatialImage
```