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How to add H/E image and alignment file to a pre-existing anndata object?

Status: Open.

#349 In BiomedicalMachineLearning/stLearn;

· thisismuskaangupta opened on May 17, 2026

Best Practice for CCI Analysis on Visium HD Data with Subset Cell Types

Status: Open.

#347 In BiomedicalMachineLearning/stLearn;

· meisproject opened on Apr 22, 2026

CCI analysis for imaging-based ST data

Status: Open.

#344 In BiomedicalMachineLearning/stLearn;

· ynpan910 opened on Mar 29, 2026

pseudotimespace_global() always yields "Connectivity is undefined for the null graph" exception

Status: Open.

#340 In BiomedicalMachineLearning/stLearn;

· marcouderzo opened on Nov 12, 2025

Workflow to Explore Trajectories from Root Cluster

Status: Open.

#332 In BiomedicalMachineLearning/stLearn;

· marcouderzo opened on Jul 15, 2025

No arrows displayed when running the Spatial trajectory inference analysis

Status: Open.

#317 In BiomedicalMachineLearning/stLearn;

· SA-coder-netizen opened on Jan 7, 2025

Read VisiumHD data through SpatialData / Support for Python 3.9

Status: Open.

#316 In BiomedicalMachineLearning/stLearn;

· marcouderzo opened on Dec 18, 2024

How to distinguish between sender spots and receiver spots? stlearn distance =200

Status: Open.

#315 In BiomedicalMachineLearning/stLearn;

· smk5g5 opened on Nov 18, 2024

st.spatial.SME.SME_normalize: ValueError: Input X contains NaN.

Status: Open.

#310 In BiomedicalMachineLearning/stLearn;

· liangyuli12138 opened on Sep 9, 2024

CCI Maps might have reversed axis labels!

Status: Open.

#309 In BiomedicalMachineLearning/stLearn;

· je71xusa opened on Jul 30, 2024

Running time of PTST analysis for Xenium data

Status: Open.

#306 In BiomedicalMachineLearning/stLearn;

· ghost opened on Jul 18, 2024

"InvalidIndexError: Reindexing only valid with uniquely valued Index objects" when running st.tl.cci.run with custom LR set

Status: Open.

#305 In BiomedicalMachineLearning/stLearn;

· je71xusa opened on Jul 15, 2024