spateo-release
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aristoteleo
Spatiotemporal modeling of spatial transcriptomics
Hi, I am trying to follow the Spateo cell segmentation tutorial, but I am throwing a ModuleNotFoundError for fbgbp at this step for segmentation: `st.cs.score_and_mask_pixels( adata, 'nuclear', k=5, method="EM+BP" )`...
Hello everyone, I re-run the analysis https://spateo-release.readthedocs.io/en/latest/tutorials/notebooks/3_cci/2_microenvironment_modeling_analysis.html#, but I got an error when running the following code ``` niche_interp = st.tl.Niche_Model( adata, group_key='Annotation', genes=targets, smooth=False, normalize=False, log_transform=False, weights_mode="knn", distr="poisson", data_id="axolotl",...
When running Since 0.8.1, cg was provided in `ot.optim.xxx`. but L119 makes the alternative importing useless. https://github.com/aristoteleo/spateo-release/blob/be1ab6d100f2ac2738dc3e379de78e494c3e8c0b/spateo/alignment/methods/paste.py#L114-L124 L119 should be the `pi, log = cg( ` to use previously imported...
question about how to plot cell segmentaion results, I follow the tutorial using different methods and parameters to segmente single cell,but how could I plot them to show the segmentation...
Dear author, I am trying to install the Spateo package and encountered an issue. I set up a conda environment with Python 3.9.0 and installed Spateo using pip install git+https://github.com/aristoteleo/spateo-release....
The boundary_line is empty when I used with `st.dd.identify_boundary` ```python bdl_img = st.dd.identify_boundary(adata=adata, spatial_key="spatial", cluster_key="leiden_0.2", bin_size=1, source_id=['1', '3'], target_id=['2', '7']) st.pl.space(adata, color=['boundary_line'], pointsize=0.2, cmap = "Reds") ```  What should...
hello,when i run the demo of Cell-cell_interaction, `weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, )` with error `AttributeError: module 'spateo.tl' has no attribute 'weighted_spatial_graph'`
Dear Authors, Thanks for your working, recently, I'm doing the 3D trajectory ,and I want to acquire the result as you showed, like this,  But I made this,as follows,...
集群无法联网，但是函数自动要联网下载，无法指定本地上传的模型 st.cs.stardist(adata, equalize=2.0, out_layer='stardist_labels') 
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Spatiotemporal modeling of spatial transcriptomics