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Ensembl gene ID versions used in Nicheformer (ENSG / ENSMUSG)

Status: Open.

#41 In theislab/nicheformer;

· cpu-yun opened on Dec 26, 2025

Pretrained Weights

Status: Open.

#40 In theislab/nicheformer;

· arbelhizmi opened on Dec 24, 2025

Inquiry Regarding Package Version Conflict in preprocess_Lu_2021.py

Status: Open.

#39 In theislab/nicheformer;

· luobimuqinyan99 opened on Dec 3, 2025

The meaning and origin about UMAP2

Status: Open.

#37 In theislab/nicheformer;

· cpu-yun opened on Nov 27, 2025

AttributeError when calling nicheformer.pp.basic_preproc()

Status: Open.

#36 In theislab/nicheformer;

· yang-lin-pp opened on Nov 24, 2025

KeyError when initializing NicheformerFineTune – missing keys in config

Status: Open.

#34 In theislab/nicheformer;

· yang-lin-pp opened on Nov 24, 2025

using Nichformer on Visium HD ?

Status: Open.

#31 In theislab/nicheformer;

· AtlasMaroc opened on Nov 12, 2025

Unable to run downstream_fine_tune.ipynb

Status: Open.

#30 In theislab/nicheformer;

· moa4020 opened on Aug 21, 2025

Fine-tuned model for Allen Brain

Status: Open.

#28 In theislab/nicheformer;

· AixinZhang-DA opened on Jul 25, 2025

get_embeddings runtime

Status: Open.

#27 In theislab/nicheformer;

· talbCgen opened on Jul 9, 2025

Installing the latest development version issue

Status: Open.

#26 In theislab/nicheformer;

· LQC-wr opened on Jun 7, 2025

How are spatial coordinates used in pretraining and downstream tasks ?

Status: Open.

#25 In theislab/nicheformer;

· TawhidMM opened on Jun 3, 2025