{"id":13511065,"url":"https://github.com/childmindresearch/bids2table","last_synced_at":"2026-01-16T11:50:13.145Z","repository":{"id":166150620,"uuid":"635935708","full_name":"childmindresearch/bids2table","owner":"childmindresearch","description":"Index BIDS datasets fast, locally or in the cloud","archived":false,"fork":false,"pushed_at":"2025-09-10T13:57:44.000Z","size":554,"stargazers_count":18,"open_issues_count":4,"forks_count":7,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-09-12T19:56:41.220Z","etag":null,"topics":["arrow","bids","neuroimaging"],"latest_commit_sha":null,"homepage":"https://childmindresearch.github.io/bids2table/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/childmindresearch.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-05-03T19:20:32.000Z","updated_at":"2025-09-10T13:56:50.000Z","dependencies_parsed_at":"2024-01-13T19:22:18.320Z","dependency_job_id":"82dbf7c5-6438-4904-9a1d-44978dcc73d4","html_url":"https://github.com/childmindresearch/bids2table","commit_stats":null,"previous_names":["childmindresearch/bids2table","cmi-dair/bids2table"],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/childmindresearch/bids2table","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/childmindresearch%2Fbids2table","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/childmindresearch%2Fbids2table/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/childmindresearch%2Fbids2table/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/childmindresearch%2Fbids2table/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/childmindresearch","download_url":"https://codeload.github.com/childmindresearch/bids2table/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/childmindresearch%2Fbids2table/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478384,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["arrow","bids","neuroimaging"],"created_at":"2024-08-01T03:00:33.349Z","updated_at":"2026-01-16T11:50:13.097Z","avatar_url":"https://github.com/childmindresearch.png","language":"Python","funding_links":[],"categories":["Data Processing","Data Processing Libraries"],"sub_categories":[],"readme":"# bids2table\n[![Build](https://github.com/childmindresearch/bids2table/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/bids2table/actions/workflows/ci.yaml?query=branch%3Amain)\n[![Docs](https://github.com/childmindresearch/bids2table/actions/workflows/docs.yaml/badge.svg?branch=main)](https://childmindresearch.github.io/bids2table/bids2table)\n[![codecov](https://codecov.io/gh/childmindresearch/bids2table/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/bids2table)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)\n\nbids2table is a library for efficiently indexing and querying large-scale BIDS neuroimaging datasets and derivatives. It aims to improve upon the efficiency of [PyBIDS](https://github.com/bids-standard/pybids) by leveraging modern data science tools.\n\nbids2table represents a BIDS dataset index as a single table with columns for BIDS entities and file metadata. The index is constructed using [Arrow](https://arrow.apache.org/) and stored in [Parquet](https://parquet.apache.org/) format, a binary tabular file format optimized for efficient storage and retrieval.\n\n## Installation\n\nA pre-release version of bids2table can be installed with\n\n```sh\npip install bids2table\n```\n\nThe latest development version can be installed with\n\n```sh\npip install git+https://github.com/childmindresearch/bids2table.git\n```\n\n## Documentation\n\nOur documentation is [here](https://childmindresearch.github.io/bids2table/).\n\n## Example\n\n```python\nimport pandas as pd\n\nfrom bids2table import bids2table\n\n# Load in memory as pandas dataframe\ndf = bids2table(\"/path/to/dataset\")\n\n# Load in parallel and stream to disk as a Parquet dataset\ndf = bids2table(\"/path/to/dataset\", persistent=True, workers=8)\n```\n\nSee [here](example/example.ipynb) for a more complete example.\n\n## Performance\n\nbids2table significantly outperforms both [PyBIDS](https://github.com/bids-standard/pybids) and [ancpBIDS](https://github.com/ANCPLabOldenburg/ancp-bids) in terms of indexing run time, index size on disk, and query run time.\n\n### Indexing performance\n\nIndexing run time and index size on disk for the [NKI Rockland Sample](https://fcon_1000.projects.nitrc.org/indi/pro/nki.html) dataset. See the [indexing benchmark](benchmark/indexing) for more details.\n\n| Index | Num workers | Run time (s) | Index size (MB) |\n| -- | -- | -- | -- |\n| PyBIDS | 1 | 1618 | 448 |\n| ancpBIDS | 1 | 465 | -- |\n| bids2table | 1 | 402 | 4.02 |\n| bids2table | 8 | 53.2 | **3.84** |\n| bids2table | 64 | **10.7** | 4.82 |\n\n\n### Query performance\n\nQuery run times for the [Chinese Color Nest Project](http://deepneuro.bnu.edu.cn/?p=163) dataset. See the [query benchmark](benchmark/query) for more details.\n\n| Index | Get subjects (ms) | Get BOLD (ms) | Query metadata (ms) | Get morning scans (ms) |\n| -- | -- | -- | -- | -- |\n| PyBIDS | 1350 | 12.3 | 6.53 | 34.3 |\n| ancpBIDS | 30.6 | 19.2 | -- | -- |\n| bids2table | **0.046** | **0.346** | **0.312** | **0.352** |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchildmindresearch%2Fbids2table","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchildmindresearch%2Fbids2table","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchildmindresearch%2Fbids2table/lists"}