stereo2xenium 0.2.3

Convert Stereo-seq data to 10X Genomics Xenium format.

install

conda activate 
pip install stereo2xenium

usage

inDir="/media/dell/data2/Stereo/eyeball/mmEyeBall/outs/feature_expression"
outDir="/media/dell/data2/Stereo/eyeball/toXenium"
SN=C04687E314
stereo2xenium convert --input ${inDir} --output ${outDir} --sample ${SN} --genome GRCm39 --cellbin_gem
stereo2xenium viewh5 --h5file ${inDir}/C04687E314.adjusted.cellbin.gef

rotate and flip

# determine the rotation angle 调整旋转角度
file="/media/dell/scRNA/spatial/Stereo/brainC04042E3/outs/visualization/C04042E3.adjusted.cellbin.gef"
outDir="/media/dell/scRNA/spatial/Stereo/brainC04042E3/toXenium"
# plot cell centroids without rotation
stereo2xenium plotRotation --file ${file} --output ${outDir} 
# try different theta value to rotate the image clockwisely or anticlockwisely.
stereo2xenium plotRotation --file ${file} --output ${outDir} --theta 138 --anticlockwise 

# Run stereo2xenium with proper theta values. 
# All of the coordination, including cell centroids, cell boundaries, and transcripts, will be rotated.
inDir="/media/dell/scRNA/spatial/Stereo/brainC04042E3/outs/visualization"   
outDir="/media/dell/scRNA/spatial/Stereo/brainC04042E3/toXenium"   
SN="C04042E3"  

stereo2xenium convert --input ${inDir} --output ${outDir} --sample ${SN} --segmentation 'HE' --genome mm10 --anticlockwise --theta 130

Mapping molecules to cells

1. The stereo-seq output data typically does not include the cellbin.gem file, which is required for mapping molecules to cells.

2. To generate this file, first run saw convert to retrieve the cellbin.gem. Then, run stereo2xenium convert to process the data.

3. If stereo2xenium convert has already been executed, you can run stereo2xenium getTranscripts separately to complete the mapping of molecules to cells.

4. Warning:

   Mapping molecules to cells is time- and memory-intensive and is not required for downstream analysis.

   You can skip it by running stereo2xenium convert without --cellbin_gem.

inDir=/media/dell/scRNA/spatial/Stereo/brainC04042E3/outs/visualization
SN=C04042E3

saw convert --threads-num 16 gef2gem --bin-size 1 \
--gef ${inDir}/${SN}.tissue.gef \
--cellbin-gef ${inDir}/${SN}.adjusted.cellbin.gef \
--cellbin-gem ${inDir}/${SN}.adjusted.cellbin.gem 

gzip ${inDir}/${SN}.adjusted.cellbin.gem

stereo2xenium convert --input ${inDir} --output ${outDir} --sample ${SN} --segmentation 'HE' --genome mm10 --cellbin_gem --anticlockwise --theta 130

stereo2xenium getTranscripts --input ${inDir} --sample ${SN} --output ${outDir} --cellbin_gem --theta 130 --anticlockwise