spateo-release
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aristoteleo
Spatiotemporal modeling of spatial transcriptomics
Hello, I'm trying to build a 3D model using my own spatial slice information, the integration process is as follows, the slices have been aligned `adata_list_coords = [adata.obsm['align_spatial_3d'] for adata...
```python aligned_slices, pis = st.align.paste_align( models=[slice1.to_memory() for slice1 in slices], spatial_key="spatial", key_added="align_spatial", device="cpu" ) ``` ``` --------------------------------------------------------------------------- KeyError Traceback (most recent call last) Cell In[8], line 1 ----> 1 aligned_slices,...
when running 'st.align.morpho_align_ref'. for "Alignment of 3D models of two stages", The other day, I upgraded the latest version of github software， I met the error: NameError. Traceback (most recent...
align_preprocess in spateo/alignment/methods/deprecated_utils.py miss one parameter 'layer'
In spateo.io.bgi.read_bgi_agg: Parameters: path Path to read file. stain_path Path to nuclei staining image. Must have the same coordinate system as the read file. If the nuclei staining image and...
Dears, Thanks for your great working for spateo. I have a question about how to make two mesh VTK data combine to one VTK data, so I could only read...
`st.tdr.models.models_backbone.backbone_methods.PrinCurve_method` run into errors with newest `tensorflow`. It's necessary to use `tensorflow==2.11.0 keras==2.11`. Error reports: ``` File ~/miniconda3/envs/spateo_updated/lib/python3.9/site-packages/spateo/tdr/models/models_backbone/backbone_methods.py:116, in NLPCA.create_model(self, num_dim, nodes, lr) 113 # Create layers: 114 # Function...
when run `morphofield_gp`, I found there is no `norm_dict` and `kernel_dict ` in [`morpho_class.py`](https://github.com/aristoteleo/spateo-release/blob/22220c57f8d501663be23c8f948dd310b505ca3d/spateo/alignment/methods/morpho_class.py#L1472C18-L1472C24) ``` File ~/miniconda3/envs/spateo/lib/python3.9/site-packages/spateo/tdr/morphometrics/morphofield/gaussian_process.py:102, in _gp_velocity(X, vf_dict) 100 def _gp_velocity(X: np.ndarray, vf_dict: dict) -> np.ndarray: 101 #...
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Spatiotemporal modeling of spatial transcriptomics