Issues

• mod.train() error

  bug
  BayraktarLab/cell2location#446 · Filter by author yitengfei120011 opened on Sep 11, 2026

• How to decide on present/non present cell types of each spot?

  question
  BayraktarLab/cell2location#441 · Filter by author maryam2079 opened on May 12, 2026
  2

• Common genes is necessary?

  question
  BayraktarLab/cell2location#440 · Filter by author frumP774 opened on May 12, 2026

• chunking large datasets

  question
  BayraktarLab/cell2location#439 · Filter by author yuu342 opened on May 11, 2026

• proximity

  question
  BayraktarLab/cell2location#437 · Filter by author Sophielsn opened on Mar 10, 2026

• model load: Missing key(s) in state_dict

  bug
  BayraktarLab/cell2location#430 · Filter by author aowenson-imm opened on Nov 27, 2025
  4

• Is it feasible to use cell2location to distinguish between malignant and non-malignant states of the same cell type?

  question
  BayraktarLab/cell2location#429 · Filter by author nihaoWX opened on Nov 18, 2025
  2

• Expected value argument (Tensor of shape (2500, 12666))

  bug
  BayraktarLab/cell2location#428 · Filter by author nine-sarayut opened on Nov 14, 2025
  1

• Does cell2location support multi-gpu ?

  question
  BayraktarLab/cell2location#426 · Filter by author AtlasMaroc opened on Nov 8, 2025
  2

• Xenium

  enhancement
  BayraktarLab/cell2location#422 · Filter by author Sophielsn opened on Sep 30, 2025
  2

• Runtime differences in version 0.1.3 and 0.1.4. [related to batch_size=None and training on large data - see issue #365]

  FAQ
  BayraktarLab/cell2location#421 · Filter by author YSqkr-ep opened on Sep 25, 2025
  4

• Questions when following the official tutorial (use_gpu, samples attribute, QC plotting)

  bug
  BayraktarLab/cell2location#417 · Filter by author asmlgkj opened on Sep 4, 2025
  2

• ValueError: at site "data_target", invalid log_prob shape

  question
  BayraktarLab/cell2location#416 · Filter by author nextgenius-ai opened on Aug 30, 2025
  2

• How to make make more CPU work in cell2location?

  question
  BayraktarLab/cell2location#415 · Filter by author Rong-ao opened on Aug 28, 2025
  1

• Error saving anndata object with cell-type specific expression of every gene in the spatial data (needed for NCEM)

  bug
  BayraktarLab/cell2location#412 · Filter by author quiquevb23 opened on Jul 30, 2025
  2

• Invalid log_prob shape

  bug
  BayraktarLab/cell2location#411 · Filter by author HarryZhang1224 opened on Jul 18, 2025
  5

• RuntimeError：expected mat1 and mat2 to have the same dtype, but got: long int != float

  bug
  BayraktarLab/cell2location#410 · Filter by author Johnny3333 opened on Jul 12, 2025
  2

• Apple Silicon MPS not detected for model training, falling back to CPU

  bug
  BayraktarLab/cell2location#408 · Filter by author clanna opened on Jun 25, 2025
  2

• MPS (Apple Silicon) TypeError: Cannot convert MPS Tensor to float64 - cell2location training fails

  bug
  BayraktarLab/cell2location#406 · Filter by author Kleinzhang99 opened on May 30, 2025
  1

• mod = RegressionModel(adata_ref) Not Working

  question
  BayraktarLab/cell2location#405 · Filter by author HDEzhsw opened on Apr 23, 2025

• OutOFMemory when loading trained mod, even in the same env [related to batch_size=None and training on large data - see issue #365]

  FAQ
  BayraktarLab/cell2location#404 · Filter by author parkjooyoung99 opened on Apr 8, 2025
  8

• IndexError: Dimension specified as 0 but tensor has no dimensions

  bug
  BayraktarLab/cell2location#403 · Filter by author iaaka opened on Apr 4, 2025
  3

• AssertionError: malformed ParamStore state - when loading saved model

  bug
  BayraktarLab/cell2location#402 · Filter by author marcouderzo opened on Apr 4, 2025
  1

• Celltypes distribution is too balanced on VisiumHD

  question
  BayraktarLab/cell2location#401 · Filter by author ConstensouxAlexis opened on Apr 2, 2025

• Error during model training

  question
  BayraktarLab/cell2location#400 · Filter by author Florian1706 opened on Mar 19, 2025
  2