SpaceHack2022-Xenium
Our team work on Xenium data for the SpaceHack 2022
Resources
Slides
Biohakcathon 2022::Xenium omni-workflow (a potential plan)
infrastructure --> Luca and Gleb | Txsim/MCMICRO
- having a single step-wise workflow
- effect of method choice for each step
Segmentation refinement by integration --> Gleb and Art1m | Txsim/MCMICRO
- Other segmentation methods
- Using the H&E image
Robustness --> Luca and Gleb | Txsim/MCMICRO
- robustness to noise at each step
- Simulation by subseting
- Simulation by purturbing segmentation boundries
- Xenium to ISS transformation simulation
Initial QC metrics --> Elyas and Art0m | Txsim/MCMICRO
- scFFPEseq vs. scRNAseq vs. Xenium
- cell type transferability
Importing Xenium in spatialdata--> Luca, Gleb, and Art1m
- alignment with and deconvolution of visium
- alignment with h&e and ROI selection
Automatic ROI/niche selection from xenium --> Elyas and Art1m
- evaluation with H&E
Gene panel selection --> Elyas and Art0m
- gene module
- spatially variable genes
- Visium deconv.
Cell typing --> Elyas, Art0m, Olga | Txsim/MCMICRO
- defining QC metrics
- maybe look into SpatialTX
Finding clones in space --> Art0m and Olga
- H&E annotation for ducts/domains
- Visium based + Xenium + H&E
Post processing --> Elays and Art0m
- ideas for cell-cell comm.