Issues

How to add H/E image and alignment file to a pre-existing anndata object?
BiomedicalMachineLearning/stLearn#349 · opened on May 17, 2026
2
Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types
BiomedicalMachineLearning/stLearn#347 · opened on Apr 22, 2026
CCI analysis for imaging-based ST data
BiomedicalMachineLearning/stLearn#344 · opened on Mar 29, 2026
pseudotimespace_global() always yields "Connectivity is undefined for the null graph" exception
BiomedicalMachineLearning/stLearn#340 · opened on Nov 12, 2025
Workflow to Explore Trajectories from Root Cluster
BiomedicalMachineLearning/stLearn#332 · opened on Jul 15, 2025
8
No arrows displayed when running the Spatial trajectory inference analysis
BiomedicalMachineLearning/stLearn#317 · opened on Jan 7, 2025
2
Read VisiumHD data through SpatialData / Support for Python 3.9
BiomedicalMachineLearning/stLearn#316 · opened on Dec 18, 2024
How to distinguish between sender spots and receiver spots? stlearn distance =200
BiomedicalMachineLearning/stLearn#315 · opened on Nov 18, 2024
st.spatial.SME.SME_normalize: ValueError: Input X contains NaN.
BiomedicalMachineLearning/stLearn#310 · opened on Sep 9, 2024
CCI Maps might have reversed axis labels!
BiomedicalMachineLearning/stLearn#309 · opened on Jul 30, 2024
1
Running time of PTST analysis for Xenium data
BiomedicalMachineLearning/stLearn#306 · opened on Jul 18, 2024
3
"InvalidIndexError: Reindexing only valid with uniquely valued Index objects" when running st.tl.cci.run with custom LR set
BiomedicalMachineLearning/stLearn#305 · opened on Jul 15, 2024
1
Image path when creating st object from other packages
BiomedicalMachineLearning/stLearn#303 · opened on Jul 3, 2024
visium HD application
BiomedicalMachineLearning/stLearn#301 · opened on Jul 1, 2024
2
Handling Large Datasets in stLearn and the Impact on Computational Performance
BiomedicalMachineLearning/stLearn#298 · opened on Jun 18, 2024