cytomining/CytoTable

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Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.

Stars: 21
Forks: 6
Open beginner issues: 0
Indexed issues: 81
Avg merge: 2d 3h
Merged PRs (30d): 6

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 2, 2026
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

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81 open issues indexed

Detect compartments in the single cell input file and throw a warning if they are not used Open

bug enhancement

cytomining/CytoTable#428 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Explore output paths for cloud-based object storage (s3-like) Open

enhancement

cytomining/CytoTable#9 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Allow data source filtering by directory structure Open

enhancement

cytomining/CytoTable#12 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enhance compartment schema specification for compartment data source groups Open

enhancement

cytomining/CytoTable#16 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Document system and workflow architecture options Open

documentation

cytomining/CytoTable#17 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Account for CellProfiler data schema differences across versions Open

enhancement

cytomining/CytoTable#20 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add pytest markers indicating relative size of tests Open

enhancement

cytomining/CytoTable#23 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable profile feature data filtering capabilities Open

enhancement

cytomining/CytoTable#24 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enhance documentation and typing for interface composability Open

documentation enhancement

cytomining/CytoTable#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Explore the use of schema for input or output specification Open

enhancement

cytomining/CytoTable#27 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Resolve potential datetime schema concatenation challenges Open

cytomining/CytoTable#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Develop a cytotable.annotate function to incorporate metadata Open

enhancement question

cytomining/CytoTable#44 · 7 comments · 1 reaction · 1 assignee · Indexed Sep 15, 2026
Improve exception visibility within console Open

enhancement

cytomining/CytoTable#54 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enhance convert() default or unspecified parameters with preferential choices Open

enhancement

cytomining/CytoTable#58 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
no_sign_request=True does not skip AWS config ID Open

cytomining/CytoTable#61 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Refine SQL table references for joins parameter Open

enhancement

cytomining/CytoTable#63 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enhance preset capabilities through JSON or similar Open

enhancement

cytomining/CytoTable#66 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Explore the use expanded column-focused data source operations Open

enhancement

cytomining/CytoTable#67 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Loading file from AWS with CytoTable will not show parquet output Open

cytomining/CytoTable#69 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Explore the use of cloud-based SQLite querying Open

enhancement

cytomining/CytoTable#70 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Plate logo in docs/source/_static Open

cytomining/CytoTable#74 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Explore the use of symbolic SQL builder for query generation and implementation Open

enhancement

cytomining/CytoTable#77 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Chunk_size parameter when using with preset + joins variables causes ordering of `Metadata_ImageNumber` column Open

cytomining/CytoTable#85 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Ensure function docstring compatibility for Sphinx v7.x Open

enhancement

cytomining/CytoTable#100 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Lint internal SQL as part of automated checks Open

enhancement

cytomining/CytoTable#107 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use automated dependency checkers to alert and update dependencies Open

enhancement

cytomining/CytoTable#110 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
parsl.dataflow.errors.JoinError: Join failure for task 1 with failed join dependencies Open

bug

cytomining/CytoTable#111 · 6 comments · 1 reaction · 1 assignee · Indexed Sep 15, 2026
Update `identifying_cols` to use `ObjectNumber` reference within presets Open

enhancement

cytomining/CytoTable#115 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Dependency conflicts with CytoTable and `pandas==2.1.1` Open

bug

cytomining/CytoTable#116 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Integrate IN Carta data ouput as input for CytoTable Open

enhancement

cytomining/CytoTable#136 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Assess and document Windows OS compatibility Open

dependencies

cytomining/CytoTable#137 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable automatic `local_cache_dir` specification for cloud-based SQLite data sources Open

enhancement

cytomining/CytoTable#140 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`parsl.jobs.errors.TooManyJobFailuresError` sporadically occurs on MacOS Images for GitHub Actions jobs during `pytest` operations Open

bug

cytomining/CytoTable#143 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add data source filenames and directories to CytoTable metadata (or similar) Open

enhancement

cytomining/CytoTable#149 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Simplify data output to single directory or filepath Open

enhancement

cytomining/CytoTable#150 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Address IN Carta data output when `concat=False` Open

enhancement

cytomining/CytoTable#154 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`WorkerLost: Task failure due to loss of worker` Failure during join data creation using HTE Parsl config with `SQ00014613.sqlite` Open

bug

cytomining/CytoTable#169 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Outline the best settings for Parsl configuration with CytoTable Open

enhancement

cytomining/CytoTable#176 · 7 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Explore pyarrow parquet write_dataset Open

enhancement

cytomining/CytoTable#177 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Document Parsl SlurmProvider usage for CU Alpine HPC Open

documentation enhancement

cytomining/CytoTable#179 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use OpenLineage API (or other similar tooling) as basis for CytoTable Paquet metadata output Open

enhancement

cytomining/CytoTable#180 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add SBOM file to repository Open

enhancement

cytomining/CytoTable#185 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Verify how large floating-point numbers are exported Open

question

cytomining/CytoTable#187 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Consistently handle `Metadata_Well` and `Metadata_Plate` column renaming and join specification Open

enhancement

cytomining/CytoTable#189 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add capability to sample source datasets by percent or rowcount to increase speed of testing Open

enhancement

cytomining/CytoTable#190 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable `_concat_source_group` single file pass-through to avoid rewrites Open

enhancement

cytomining/CytoTable#191 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Provide data statistics report as part of CytoTable output Open

enhancement

cytomining/CytoTable#200 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Define ideal compartment and metadata table relationships for joins to avoid returning NA results Open

enhancement

cytomining/CytoTable#201 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Retain extracted, unjoined table output when joining data in CytoTable Open

enhancement

cytomining/CytoTable#202 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Extract or somehow store data from CellProfiler `experiment` tables in CytoTable output Open

enhancement

cytomining/CytoTable#203 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

cytomining/CytoTable

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