Issues

• What is the maximum number of cell types that can be annotated in a single run when using scVI and Geneformer via Census?

  chanzuckerberg/cellxgene-census#1460 · Filter by author CajoleU opened on May 6, 2026

• scvi-train.py reads n_hidden from config but never passes it to the constructor

  bug
  chanzuckerberg/cellxgene-census#1459 · Filter by author gokceneraslan opened on Mar 22, 2026
  1

• TileDB index of scvi embeddings for 2025-11-08 version

  bug
  chanzuckerberg/cellxgene-census#1457 · Filter by author rastogiruchir opened on Feb 4, 2026
  2

• tiledbsoma 2.2.0 breaks user-agent in requests

  bug
  chanzuckerberg/cellxgene-census#1451 · Filter by author ivirshup opened on Dec 16, 2025

• dataset count distribution column was deprecated [R]

  chanzuckerberg/cellxgene-census#1450 · Filter by author myushen opened on Dec 16, 2025

• scVI hyperparameter tuning

  discovery
  chanzuckerberg/cellxgene-census#1444 · Filter by author mlin opened on Nov 12, 2025

• builder: merge/refactor census_summary modules

  tech
  chanzuckerberg/cellxgene-census#1442 · Filter by author mlin opened on Nov 8, 2025

• Consider changes to differentiate how modalities are presented or summarized

  census schemadiscovery
  chanzuckerberg/cellxgene-census#1441 · Filter by author brianraymor opened on Nov 7, 2025

• Update assay lists in globals.py

  chanzuckerberg/cellxgene-census#1432 · Filter by author brianraymor opened on Oct 21, 2025
  1

  

• Add modeling for descendants of organisms

  census schemadiscovery
  chanzuckerberg/cellxgene-census#1425 · Filter by author brianraymor opened on Oct 7, 2025
  

• Review and update spatial sections

  census schema
  chanzuckerberg/cellxgene-census#1410 · Filter by author brianraymor opened on Aug 6, 2025
  2

  

• Review and update Census Docsite schema

  census schemadocumentation
  chanzuckerberg/cellxgene-census#1408 · Filter by author brianraymor opened on Aug 5, 2025
  

• Draft updates to list of accepted assays and their categories

  census schema
  chanzuckerberg/cellxgene-census#1405 · Filter by author brianraymor opened on Jul 24, 2025
  9

  

• H1 Goal 3.2: Accelerate a biology researcher’s ability to build, reuse, and validate models.

  chanzuckerberg/cellxgene-census#1400 · Filter by author kaloster opened on Jun 9, 2025

• Dataset e51bae9a-c747-4b64-904a-4da7cda218ab not available via API

  chanzuckerberg/cellxgene-census#1396 · Filter by author GKild opened on May 28, 2025
  4

• get_seurat() gets scvi embedding in 2023-12-15 Census, but not in 2024-07-01 or 2025-01-30 versions

  bug
  chanzuckerberg/cellxgene-census#1393 · Filter by author DaniilSarkisyan opened on May 8, 2025

• Census schema version incorrect

  bug
  chanzuckerberg/cellxgene-census#1384 · Filter by author ivirshup opened on Mar 31, 2025

• Doc updates for disease terms with schema 6.0

  tech
  chanzuckerberg/cellxgene-census#1379 · Filter by author ivirshup opened on Mar 26, 2025

• Incorrect number of donors in census["census_info"]["summary"]

  bug
  chanzuckerberg/cellxgene-census#1373 · Filter by author ivirshup opened on Mar 17, 2025
  1

• Fix flaky text fixture in builder

  tech
  chanzuckerberg/cellxgene-census#1372 · Filter by author ivirshup opened on Mar 13, 2025

• Census Spatial must be updated to support new Visium versions

  5.3
  chanzuckerberg/cellxgene-census#1364 · Filter by author brianraymor opened on Mar 3, 2025

• Census Spatial 2025 Q1

  epictech
  chanzuckerberg/cellxgene-census#1360 · Filter by author brianraymor opened on Feb 21, 2025

• API equivalence across spatial and single cell

  spatialuser request
  chanzuckerberg/cellxgene-census#1359 · Filter by author ivirshup opened on Feb 21, 2025

• is the published geneformer for census 2024-07-01 fine-tuned

  bug
  chanzuckerberg/cellxgene-census#1355 · Filter by author vtrifonov-altos opened on Feb 12, 2025
  2

• ExperimentDataPipe workers don't seem to share memory

  bug
  chanzuckerberg/cellxgene-census#1353 · Filter by author yanwu2014 opened on Feb 10, 2025