Issues

• Enable remote SQLite references

  Feature

  cytomining/CytoTable#485 · Filter by author d33bs opened on Jul 7, 2026

• NameError: Cytotable not defined

  cytomining/CytoTable#476 · Filter by author CesannevdM opened on Jun 22, 2026
  3

• Find a way for users to avoid SQL configurations

  cytomining/CytoTable#454 · Filter by author d33bs opened on May 13, 2026
  1

• Question: Best practices to limit CPU usage?

  cytomining/CytoTable#437 · Filter by author jashapiro opened on Apr 14, 2026
  5

• Refactor convert.py with greater modularity

  Task

  cytomining/CytoTable#430 · Filter by author d33bs opened on Mar 26, 2026

• Image features and important Metadata fields missing from parquets

  question
  cytomining/CytoTable#425 · Filter by author kate-bowers-broad opened on Mar 19, 2026
  5

• Check for empty or zero row tables (provide specific warning)

  Bug

  cytomining/CytoTable#409 · Filter by author d33bs opened on Jan 23, 2026

• Fail to summarize across plate

  cytomining/CytoTable#377 · Filter by author GaiaGerbaka opened on Oct 6, 2025
  3

• Can't run examplehuman

  question
  cytomining/CytoTable#374 · Filter by author ErinWeisbart opened on Oct 3, 2025
  7

• Consider use of pyarrow.lib.RecordBatchReader for internal streamable data handling

  Feature

  cytomining/CytoTable#371 · Filter by author d33bs opened on Sep 30, 2025

• Using compartments to input CSVs with custom names

  question
  Feature

  cytomining/CytoTable#362 · Filter by author GaiaGerbaka opened on Sep 10, 2025
  6

• New CytoTable preset?

  Feature

  cytomining/CytoTable#358 · Filter by author jenna-tomkinson opened on Sep 2, 2025
  2

  

• Add anndata input capabilities

  Feature

  cytomining/CytoTable#347 · Filter by author d33bs opened on Aug 11, 2025

• Error when a cell-nucleus pair does not exists: IndexError: list index out of range

  bugenhancement
  Bug

  cytomining/CytoTable#339 · Filter by author MikeLippincott opened on Jun 25, 2025
  1

• Add code coverage details to readme

  documentation
  Feature

  cytomining/CytoTable#336 · Filter by author d33bs opened on Jun 20, 2025

• Cleanup parsl logging directory and make unique by default for concurrent usage

  Bug

  cytomining/CytoTable#330 · Filter by author d33bs opened on May 30, 2025
  3

• Migrate from mypy to ty for type linting

  enhancement
  Task

  cytomining/CytoTable#329 · Filter by author d33bs opened on May 30, 2025

• Add DuckDB as a data source

  Feature

  cytomining/CytoTable#319 · Filter by author d33bs opened on May 9, 2025

• Add Parquet as a data source

  Feature

  cytomining/CytoTable#318 · Filter by author d33bs opened on May 9, 2025

• Add command-line interface (CLI)

  enhancement
  Feature

  cytomining/CytoTable#316 · Filter by author d33bs opened on May 5, 2025

• Add PathName as default to extract for CytoTable

  enhancement
  Feature

  cytomining/CytoTable#305 · Filter by author jenna-tomkinson opened on Mar 24, 2025

• How do we determine what CellProfiler features are metadata or not?

  question
  cytomining/CytoTable#294 · Filter by author jenna-tomkinson opened on Feb 3, 2025
  1

• Add single-cell images to output

  enhancement
  cytomining/CytoTable#262 · Filter by author d33bs opened on Nov 18, 2024

• Add Lance output option

  enhancement
  cytomining/CytoTable#261 · Filter by author d33bs opened on Nov 18, 2024

• Installation may hang for long periods during dependency resolutions for boto3 or botocore

  enhancement
  cytomining/CytoTable#224 · Filter by author d33bs opened on Sep 3, 2024