Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-20 05:03 UTC

cytomining / pycytominer

Python package for image-based profiling

Python · Jupyter NotebookBSD-3-Clause★ 145 stars⑂ 42 forkssince Jul 2019View on GitHub ↗

KindCommand-line toolLibraryhow this is determined

#cytominer #microscopy #morphological-profiling #python #cellprofiler #image-analysis #image-based-profiling

cytomining/pycytominer holds a health index of 94 out of 100, placing it in the Exceptional band. It scores highest on Engineering Quality (96/100) and lowest on AI Readiness (64/100). It was last updated 1 day ago. 2 contributors account for most of its recent work.

overall / 100

Exceptional

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.

Exceptional93-100The record's top tier (≈ top 5%); essentially all checked criteria met

Excellent80-92Strong across the board; minor gaps

Good65-79Healthy; gaps are limited and manageable

Moderate50-64Acceptable with notable gaps; review recommended

Weak35-49Material weaknesses across several areas

At Risk20-34Significant weaknesses; adoption warrants caution

Critical1-19Severe problems (abandoned, single-maintainer, no hygiene)

Score profile

Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.

The weighted overall 81 is calibrated to 94 on the published index scale (record calibration 2026-08-02).

Ownership

CytominingOrganization

41 followers28 public repossince May 2016

This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.

Package ecosystems

Registry	Package	Version	Downloads / mo	Versions	Last publish
PyPI	pycytominer	1.7.1	2,226	19	37 days ago

Metrics by category

Vitality

Is the project alive — is code being written and are releases shipping?

93Exceptional · 21% of overall

Development activity

89Excellent

How it's scored

36/36	Push recency — last push 1 days ago
24.9/36	Commit cadence — 36/52 weeks with commits
18/18	Commit volume — 135 commits in the last year
10/10	OpenSSF Scorecard: Maintained — 30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10

Inputs used

commits_last_year	135
human_commit_share	0.42
days_since_last_push	1
active_weeks_last_year	36

Release discipline

100Exceptional

How it's scored

27/27	Ships releases — 20 releases published
36/36	Release recency — latest release 37 days ago
27/27	Release cadence — a release every ~41.3 days
0/10	OpenSSF Scorecard: Signed-Releases — no data

Inputs used

releases_count	20
latest_release_tag	v1.7.1
releases_from_tags	no
days_since_latest_release	37
mean_days_between_releases	41.3

Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.

Community & Adoption

Does the project have users, downloads, attention, and a welcoming setup for contributors?

66Good · 17% of overall

Popularity & adoption

50Moderate

How it's scored

35/60	Stars — 145 stars
13.4/25	Forks — 42 forks
1.7/15	Watchers — 3 watchers

Inputs used

forks	42
stars	145
watchers	3
growth_state	unverified
growth_factor_pct	100
growth_unverified_reason	no_history

Community health

92Excellent

How it's scored

22.5/22.5	README
22.5/22.5	License — recognized license (BSD-3-Clause)
18/18	CONTRIBUTING guide
13.5/13.5	Code of conduct
0/7.2	Issue template
6.3/6.3	PR template

Inputs used

has_readme	yes
has_license	yes
readme_badges	6
has_contributing	yes
has_issue_template	no
has_code_of_conduct	yes
readme_badge_services	codecov.io, github.com, readthedocs.org, shields.io
has_pull_request_template	yes

Ecosystem adoption (downloads)

56Moderate

How it's scored

44.6/80	Monthly downloads — 2,226 downloads/month across pypi
0/20	Registry dependents — not reported by this ecosystem

Inputs used

packages	pycytominer
dependents	—
ecosystems	pypi
total_downloads	—
monthly_downloads	2,226
unverified_packages_excluded	—

Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.

Sustainability & Governance

Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?

77Good · 23% of overall

Maintainer resilience (bus factor)

61Moderate

How it's scored

25.2/54	Bus factor — 2 contributor(s) cover half of all commits
12.2/22.5	Commit distribution — top contributor authored 46% of commits
13.5/13.5	Contributor breadth — 22 contributors
10/10	OpenSSF Scorecard: Contributors — project has 30 contributing companies or organizations

Inputs used

bus_factor	2
contributors_sampled	22
top_contributor_share	0.456

Issue & PR responsiveness

89Excellent

How it's scored

34.9/42	Issue resolution — 83% of issues closed
27.2/30	PR acceptance — 441/487 decided PRs merged
0/13	Newcomer PR acceptance — no first-time contributor's PR decided in 30d
15/15	OpenSSF Scorecard: Code-Review — all changesets reviewed

Inputs used

merged_prs	441
open_issues	45
closed_issues	223
prs_merged_7d	0
prs_decided_7d	0
prs_merged_30d	1
prs_decided_30d	1
issue_closed_ratio	0.832
closed_unmerged_prs	46
first_time_authors_30d	0
first_time_prs_merged_30d	0
first_time_prs_decided_30d	0

Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

64Moderate

How it's scored

30/30	Ownership backing — organization-owned
0/20	Verified domain
11.7/25	Owner reach — 41 followers of cytomining
22.6/25	Track record — 28 public repos, account ~10 yr old

Inputs used

followers	41
owner_type	Organization
is_verified	no
owner_login	cytomining
public_repos	28
account_age_days	3,782

Package maintenance

100Exceptional

How it's scored

25/25	Published & resolvable — 1 package(s) on pypi
35/35	Publish recency — latest publish 37 days ago
20/20	Version history — 19 published versions
20/20	Not deprecated — active, not deprecated or yanked

Inputs used

packages	pycytominer
ecosystems	pypi
any_deprecated	no
min_days_since_publish	37

Engineering Quality

Are baseline engineering and documentation practices in place?

96Exceptional · 19% of overall

Engineering practices

94Exceptional

How it's scored

24/24	CI workflows — 4 workflow(s)
24/24	Tests present
16/16	Linter config — pyproject.toml ([tool.ruff])
9.6/9.6	Pre-commit hooks
0/6.4	.editorconfig
20/20	OpenSSF Scorecard: CI-Tests — 27 out of 27 merged PRs checked by a CI test -- score normalized to 10

Inputs used

has_ci	yes
has_tests	yes
has_editorconfig	no
has_linter_config	yes
has_precommit_config	yes

Documentation

100Exceptional

How it's scored

30/30	README
25/25	Documentation directory
15/15	Documentation / homepage site — https://pycytominer.readthedocs.io/en/latest/
10/10	Repository description
10/10	Topics — 7 topics
10/10	Wiki

Inputs used

topics	cytominer, microscopy, morphological-profiling, python, cellprofiler, image-analysis, image-based-profiling
has_wiki	yes
homepage	https://pycytominer.readthedocs.io/en/latest/
docs_site	https://pycytominer.readthedocs.io/en/latest/
has_readme	yes
has_docs_dir	yes
has_description	yes

Security

Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?

74Good · 16% of overall

Security posture

67Good

How it's scored

7.5/7.5	Binary-Artifacts — no binaries found in the repo
0/7.5	Branch-Protection — no data
2.5/2.5	CI-Tests — 27 out of 27 merged PRs checked by a CI test -- score normalized to 10
0/2.5	CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
7.5/7.5	Code-Review — all changesets reviewed
2.5/2.5	Contributors — project has 30 contributing companies or organizations
10/10	Dangerous-Workflow — no dangerous workflow patterns detected
7.5/7.5	Dependency-Update-Tool — update tool detected
0/5	Fuzzing — project is not fuzzed
2.5/2.5	License — license file detected
7.5/7.5	Maintained — 30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10
5/5	Packaging — packaging workflow detected
0/5	Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
0/5	SAST — SAST tool is not run on all commits -- score normalized to 0
5/5	Security-Policy — security policy file detected
0/7.5	Signed-Releases — no data
0/7.5	Token-Permissions — detected GitHub workflow tokens with excessive permissions
3/7.5	Vulnerabilities — 6 existing vulnerabilities detected

Inputs used

source	openssf_scorecard
checks_evaluated	16
scorecard_version	v5.5.0
checks_inconclusive	2
scorecard_aggregate	6.7

Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.

Dependency advisories

100Exceptional

How it's scored

35/35	Direct dependencies free of known advisories — no direct dependency carries a known advisory
25/25	Indirect dependencies free of known advisories — no indirect dependency carries a known advisory
0/40	No advisories left outstanding — no advisory carries a publication date

Inputs used

source	osv
advisories	0
affected_packages	0
assessed_packages	21
unassessed_packages	0
affected_by_severity	none
direct_affected_packages	0

Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:pycytominer@1.7.1 runtime dependency closure — what installing the published package pulls in — 21 packages. Reachability is not analyzed.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.

64Moderate · 4% of overall

Agent context & guidance

40Weak

How it's scored

0/45	Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15	Machine-readable docs (llms.txt)
40/40	Legible commit history — 40 of 42 human commits state their intent (structured subject or explanatory body)

Inputs used

has_llms_txt	no
llms_txt_url	—
legible_history_share	0.952
agent_instruction_files	—
agent_instruction_max_bytes	—

Verify loop (build / test / typecheck)

73Good

How it's scored

18/18	One-command bootstrap — Makefile
22/22	Automated tests
11/11	Lint / format config — pyproject.toml ([tool.ruff])
0/11	Static type checking
10/10	Reproducible environment — devcontainer, Dockerfile, lockfile
4/10	Demonstrated agent practice — 2 of the last 100 commits agent-authored or agent-credited
8/8	Automated maintenance — 58 of the last 100 commits are automated dependency updates
0/10	OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0

Inputs used

has_nix	no
has_tests	yes
lockfiles	uv.lock
has_dockerfile	yes
typed_language	no
bootstrap_files	Makefile
has_devcontainer	yes
has_linter_config	yes
typecheck_configs	—
agent_commit_share	0.02
toolchain_manifests	—
dependency_bot_commit_share	0.58

Code legibility for models

55Moderate

How it's scored

0/45	Type-checkable code — Python without a type-check config
55/55	Manageable file sizes — 0/69 source files over 60KB

Inputs used

primary_language	Python
largest_source_bytes	44,152
source_files_sampled	69
oversized_source_files	0

Machine-readable interfaces

100Exceptional

How it's scored

0/40	API schema (OpenAPI/GraphQL/proto) — not applicable to this kind of software
0/20	MCP server — not applicable to this kind of software
40/40	Runnable examples — notebooks

Inputs used

example_dirs	notebooks
has_mcp_signal	no
api_schema_files	—
interfaces_expected_of	—

Excluded from scoring (no data or not applicable): API schema (OpenAPI/GraphQL/proto), MCP server. Remaining weights renormalized.

Key facts

145GitHub stars

22contributors

135commits, last 12 months

1days since last push

20releases

2bus factor

45open issues

PyPIpackage ecosystems

Data collection warnings

Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token

More detail

Star and fork history 0 ★ / 42 ⇿

0Stars

42Forks

19Releases

When each star and fork was added, collected from GitHub and bucketed by day. Cumulative growth sits directly above the daily additions it is made of, so the two read against each other: steady organic accretion looks nothing like an abrupt, short-lived burst. Where that difference is measurable, it is reported as growth authenticity.

Major 1Minor 8Patch 9

Each point covers 7 days.

OpenSSF Scorecard 6.7 / 10

6.7aggregate

Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).Scorecard v5.5.0 · 2026-09-20 05:02 UTC

10	Binary-Artifacts	no binaries found in the repo
n/a	Branch-Protection	internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md
10	CI-Tests	27 out of 27 merged PRs checked by a CI test -- score normalized to 10
0	CII-Best-Practices	no effort to earn an OpenSSF best practices badge detected
10	Code-Review	all changesets reviewed
10	Contributors	project has 30 contributing companies or organizations
10	Dangerous-Workflow	no dangerous workflow patterns detected
10	Dependency-Update-Tool	update tool detected
0	Fuzzing	project is not fuzzed
10	License	license file detected
10	Maintained	30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10
10	Packaging	packaging workflow detected
0	Pinned-Dependencies	dependency not pinned by hash detected -- score normalized to 0
0	SAST	SAST tool is not run on all commits -- score normalized to 0
10	Security-Policy	security policy file detected
n/a	Signed-Releases	no releases found
0	Token-Permissions	detected GitHub workflow tokens with excessive permissions
4	Vulnerabilities	6 existing vulnerabilities detected

Direct dependencies 10

Registry	Package	Version constraint	Manifest
PyPI	clevercsv	`>=0.8.5,<0.9`	pyproject.toml
PyPI	fire	`>=0.5`	pyproject.toml
PyPI	numpy	`>=1.16.5`	pyproject.toml
PyPI	pandas	`>=1.2`	pyproject.toml
PyPI	pyarrow	`>=8`	pyproject.toml
PyPI	pyyaml	`>=6`	pyproject.toml
PyPI	scikit-learn	`>=0.21.2`	pyproject.toml
PyPI	scipy	`>=1.5`	pyproject.toml
PyPI	scipy	`>=1.16.1`	pyproject.toml
PyPI	sqlalchemy	`>=1.3.6,<3`	pyproject.toml

All dependencies 294

Full resolved dependency set from the GitHub dependency graph: 11 direct and 283 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

Registry	Package	Version	Relation
PyPI	clevercsv	`0.8.5`	direct
PyPI	fire	`0.7.1`	direct
PyPI	numpy	`2.2.6`	direct
PyPI	pandas	`2.3.3`	direct
PyPI	pyarrow	`20.0.0`	direct
PyPI	pyarrow	`22.0.0`	direct
PyPI	pyyaml	`6.0.3`	direct
PyPI	scikit-learn	`1.7.2`	direct
PyPI	scipy	`1.15.3`	direct
PyPI	scipy	`1.17.1`	direct
PyPI	sqlalchemy	`2.0.52`	direct
PyPI	accessible-pygments	`0.0.5`	indirect
PyPI	agate	`1.14.2`	indirect
PyPI	agate-dbf	`0.2.4`	indirect
PyPI	agate-excel	`0.4.2`	indirect
PyPI	agate-sql	`0.7.3`	indirect
PyPI	aiobotocore	`3.7.0`	indirect
PyPI	aiohappyeyeballs	`2.6.2`	indirect
PyPI	aiohttp	`3.14.3`	indirect
PyPI	aioitertools	`0.13.0`	indirect
PyPI	aiosignal	`1.4.0`	indirect
PyPI	alabaster	`1.0.0`	indirect
PyPI	anndata	`0.11.4`	indirect
PyPI	anndata	`0.12.16`	indirect
PyPI	annotated-types	`0.7.0`	indirect
PyPI	anyio	`4.13.0`	indirect
PyPI	appnope	`0.1.4`	indirect
PyPI	array-api-compat	`1.14.0`	indirect
PyPI	asciitree	`0.3.3`	indirect
PyPI	ast-serialize	`0.6.0`	indirect
PyPI	astroid	`4.1.2`	indirect
PyPI	asttokens	`3.0.1`	indirect
PyPI	async-timeout	`5.0.1`	indirect
PyPI	attrs	`26.1.0`	indirect
PyPI	autodoc	`0.5.0`	indirect
PyPI	babel	`2.18.0`	indirect
PyPI	backports-tempfile	`1.0`	indirect
PyPI	backports-weakref	`1.0.post1`	indirect
PyPI	beautifulsoup4	`4.14.3`	indirect
PyPI	bioio	`3.3.0`	indirect
PyPI	bioio-base	`3.3.0`	indirect
PyPI	bioio-ome-tiff	`1.4.0`	indirect
PyPI	bioio-ome-zarr	`3.4.0`	indirect
PyPI	bioio-tifffile	`1.3.0`	indirect
PyPI	bleach	`6.4.0`	indirect
PyPI	boto3	`1.43.0`	indirect
PyPI	botocore	`1.43.0`	indirect
PyPI	bqplot	`0.13.1`	indirect
PyPI	bqscales	`0.3.7`	indirect
PyPI	certifi	`2026.5.20`	indirect
PyPI	cffi	`2.0.0`	indirect
PyPI	cfgv	`3.5.0`	indirect
PyPI	chardet	`7.4.3`	indirect
PyPI	charset-normalizer	`3.4.7`	indirect
PyPI	click	`8.4.1`	indirect
PyPI	cloudpickle	`3.1.2`	indirect
PyPI	codecov	`2.1.13`	indirect
PyPI	colorama	`0.4.6`	indirect
PyPI	comm	`0.2.3`	indirect
PyPI	configparser	`7.2.0`	indirect
PyPI	contourpy	`1.3.2`	indirect
PyPI	cosmicqc	`1.1.0`	indirect
PyPI	coverage	`7.14.0`	indirect
PyPI	csvkit	`1.5.0`	indirect
PyPI	cycler	`0.12.1`	indirect
PyPI	cyclopts	`4.16.1`	indirect
PyPI	cytodataframe	`0.0.30`	indirect
PyPI	cytodataframe	`0.3.1`	indirect
PyPI	cytominer-database	`0.3.4`	indirect
PyPI	dask	`2026.3.0`	indirect
PyPI	dbfread	`2.0.7`	indirect
PyPI	debugpy	`1.8.20`	indirect
PyPI	decorator	`5.3.1`	indirect
PyPI	defusedxml	`0.7.1`	indirect
PyPI	distlib	`0.4.0`	indirect
PyPI	distributed	`2026.3.0`	indirect
PyPI	docstring-parser	`0.18.0`	indirect
PyPI	docutils	`0.21.2`	indirect
PyPI	donfig	`0.8.1.post1`	indirect
PyPI	dunamai	`1.26.2`	indirect
PyPI	elementpath	`5.1.1`	indirect
PyPI	et-xmlfile	`2.0.0`	indirect
PyPI	exceptiongroup	`1.3.1`	indirect
PyPI	executing	`2.2.1`	indirect
PyPI	fasteners	`0.20`	indirect
PyPI	fastjsonschema	`2.21.2`	indirect
PyPI	filelock	`3.29.0`	indirect
PyPI	flexcache	`0.3`	indirect
PyPI	flexparser	`0.4`	indirect
PyPI	fonttools	`4.63.0`	indirect
PyPI	frozenlist	`1.8.0`	indirect
PyPI	fsspec	`2026.7.0`	indirect
PyPI	furo	`2025.12.19`	indirect
PyPI	ghp-import	`2.1.0`	indirect
PyPI	google-crc32c	`1.8.0`	indirect
PyPI	greenlet	`3.5.1`	indirect
PyPI	groundwork-sphinx-theme	`1.1.1`	indirect
PyPI	h11	`0.16.0`	indirect
PyPI	h5py	`3.16.0`	indirect
PyPI	identify	`2.6.19`	indirect
PyPI	idna	`3.16`	indirect
PyPI	imagecodecs	`2025.3.30`	indirect
PyPI	imageio	`2.37.3`	indirect
PyPI	imagesize	`2.0.0`	indirect
PyPI	importlib-metadata	`9.0.0`	indirect
PyPI	iniconfig	`2.3.0`	indirect
PyPI	ipydatawidgets	`4.3.5`	indirect
PyPI	ipykernel	`7.3.0`	indirect
PyPI	ipython	`8.39.0`	indirect
PyPI	ipyvolume	`0.6.3`	indirect
PyPI	ipyvue	`1.12.0`	indirect
PyPI	ipyvuetify	`1.11.3`	indirect
PyPI	ipywebrtc	`0.6.0`	indirect
PyPI	ipywidgets	`8.1.8`	indirect
PyPI	isodate	`0.7.2`	indirect
PyPI	jedi	`0.20.0`	indirect
PyPI	jinja2	`3.1.6`	indirect
PyPI	jmespath	`1.1.0`	indirect
PyPI	joblib	`1.5.3`	indirect
PyPI	jsonschema	`4.26.0`	indirect
PyPI	jsonschema-specifications	`2025.9.1`	indirect
PyPI	jupyter-client	`8.9.1`	indirect
PyPI	jupyter-core	`5.9.1`	indirect
PyPI	jupyterlab-pygments	`0.3.0`	indirect
PyPI	jupyterlab-widgets	`3.0.16`	indirect
PyPI	kerchunk	`0.2.10`	indirect
PyPI	kiwisolver	`1.5.0`	indirect
PyPI	lazy-loader	`0.5`	indirect
PyPI	leather	`0.4.1`	indirect
PyPI	legacy-api-wrap	`1.5`	indirect
PyPI	legacy-cgi	`2.6.4`	indirect
PyPI	librt	`0.13.0`	indirect
PyPI	llvmlite	`0.48.0`	indirect
PyPI	locket	`1.0.0`	indirect
PyPI	lxml	`6.1.1`	indirect
PyPI	lxml-html-clean	`0.4.5`	indirect
PyPI	markdown	`3.10.2`	indirect
PyPI	markdown-it-py	`3.0.0`	indirect
PyPI	markupsafe	`3.0.3`	indirect
PyPI	matplotlib	`3.10.9`	indirect
PyPI	matplotlib-inline	`0.2.2`	indirect
PyPI	mdit-py-plugins	`0.6.1`	indirect
PyPI	mdurl	`0.1.2`	indirect
PyPI	mergedeep	`1.3.4`	indirect
PyPI	mistune	`3.3.3`	indirect
PyPI	mkdocs	`1.6.1`	indirect
PyPI	mkdocs-get-deps	`0.2.2`	indirect
PyPI	mock	`5.2.0`	indirect
PyPI	more-itertools	`11.1.0`	indirect
PyPI	msgpack	`1.2.1`	indirect
PyPI	multidict	`6.7.1`	indirect
PyPI	mypy	`2.3.1`	indirect
PyPI	mypy-extensions	`1.1.0`	indirect
PyPI	myst-parser	`4.0.1`	indirect
PyPI	natsort	`8.4.0`	indirect
PyPI	nbclient	`0.10.4`	indirect
PyPI	nbconvert	`7.17.1`	indirect
PyPI	nbformat	`5.10.4`	indirect
PyPI	nbsphinx	`0.9.8`	indirect
PyPI	nest-asyncio	`1.6.0`	indirect
PyPI	nest-asyncio2	`1.7.2`	indirect
PyPI	networkx	`3.4.2`	indirect
PyPI	nodeenv	`1.10.0`	indirect
PyPI	numcodecs	`0.13.1`	indirect
PyPI	numcodecs	`0.16.5`	indirect
PyPI	olefile	`0.47`	indirect
PyPI	ome-arrow	`0.0.8`	indirect
PyPI	ome-types	`0.6.3`	indirect
PyPI	opencv-python	`4.13.0.92`	indirect
PyPI	openpyxl	`3.1.5`	indirect
PyPI	packaging	`26.2`	indirect
PyPI	pandas-stubs	`2.3.3.260113`	indirect
PyPI	pandocfilters	`1.5.1`	indirect
PyPI	parsedatetime	`2.6`	indirect
PyPI	parso	`0.8.7`	indirect
PyPI	partd	`1.4.2`	indirect
PyPI	pathspec	`1.1.1`	indirect
PyPI	pexpect	`4.9.0`	indirect
PyPI	pillow	`12.3.0`	indirect
PyPI	pint	`0.25.3`	indirect
PyPI	platformdirs	`4.9.6`	indirect
PyPI	pluggy	`1.6.0`	indirect
PyPI	pooch	`1.9.0`	indirect
PyPI	pre-commit	`4.6.2`	indirect
PyPI	prompt-toolkit	`3.0.51`	indirect
PyPI	propcache	`0.5.2`	indirect
PyPI	psutil	`7.2.2`	indirect
PyPI	ptyprocess	`0.7.0`	indirect
PyPI	pure-eval	`0.2.3`	indirect
PyPI	pycparser	`3.0`	indirect
PyPI	pydantic	`2.13.4`	indirect
PyPI	pydantic-core	`2.46.4`	indirect
PyPI	pydantic-extra-types	`2.11.1`	indirect
PyPI	pygments	`2.20.0`	indirect
PyPI	pyparsing	`3.3.2`	indirect
PyPI	pytest	`9.1.1`	indirect
PyPI	pytest-cov	`7.1.0`	indirect
PyPI	python-dateutil	`2.9.0.post0`	indirect
PyPI	python-discovery	`1.3.1`	indirect
PyPI	python-slugify	`8.0.4`	indirect
PyPI	pythreejs	`2.4.2`	indirect
PyPI	pytimeparse	`1.1.8`	indirect
PyPI	pytz	`2026.2`	indirect
PyPI	pyvista	`0.48.4`	indirect
PyPI	pywavelets	`1.8.0`	indirect
PyPI	pyyaml-env-tag	`1.1`	indirect
PyPI	pyzmq	`27.1.0`	indirect
PyPI	referencing	`0.37.0`	indirect
PyPI	regex	`2026.5.9`	indirect
PyPI	requests	`2.34.2`	indirect
PyPI	rich	`15.0.0`	indirect
PyPI	rich-rst	`2.0.1`	indirect
PyPI	rpds-py	`0.30.0`	indirect
PyPI	ruff	`0.16.5`	indirect
PyPI	s3fs	`2026.7.0`	indirect
PyPI	s3transfer	`0.17.0`	indirect
PyPI	scikit-image	`0.25.2`	indirect
PyPI	scooby	`0.11.2`	indirect
PyPI	scverse-misc	`0.0.3`	indirect
PyPI	seaborn	`0.13.2`	indirect
PyPI	semver	`3.0.4`	indirect
PyPI	session-info2	`0.4.1`	indirect
PyPI	setuptools	`69.5.1`	indirect
PyPI	six	`1.17.0`	indirect
PyPI	snowballstemmer	`3.0.1`	indirect
PyPI	sortedcontainers	`2.4.0`	indirect
PyPI	soupsieve	`2.9`	indirect
PyPI	sphinx	`8.1.3`	indirect
PyPI	sphinx-autoapi	`3.8.1`	indirect
PyPI	sphinx-autobuild	`2024.10.3`	indirect
PyPI	sphinx-basic-ng	`1.0.0b2`	indirect
PyPI	sphinx-copybutton	`0.5.2`	indirect
PyPI	sphinx-togglebutton	`0.4.5`	indirect
PyPI	sphinxcontrib-applehelp	`2.0.0`	indirect
PyPI	sphinxcontrib-devhelp	`2.0.0`	indirect
PyPI	sphinxcontrib-htmlhelp	`2.1.0`	indirect
PyPI	sphinxcontrib-jsmath	`1.0.1`	indirect
PyPI	sphinxcontrib-mermaid	`2.1.0`	indirect
PyPI	sphinxcontrib-qthelp	`2.0.0`	indirect
PyPI	sphinxcontrib-serializinghtml	`2.0.0`	indirect
PyPI	stack-data	`0.6.3`	indirect
PyPI	starlette	`1.3.1`	indirect
PyPI	tabulate	`0.10.0`	indirect
PyPI	tblib	`3.2.2`	indirect
PyPI	termcolor	`3.3.0`	indirect
PyPI	text-unidecode	`1.3`	indirect
PyPI	threadpoolctl	`3.6.0`	indirect
PyPI	tifffile	`2025.5.10`	indirect
PyPI	tifffile	`2026.3.3`	indirect
PyPI	tinycss2	`1.4.0`	indirect
PyPI	tomli	`2.4.1`	indirect
PyPI	toolz	`1.1.0`	indirect
PyPI	tornado	`6.5.8`	indirect
PyPI	traitlets	`5.15.0`	indirect
PyPI	traittypes	`0.2.3`	indirect
PyPI	trame	`3.13.2`	indirect
PyPI	trame-client	`3.12.3`	indirect
PyPI	trame-common	`1.2.3`	indirect
PyPI	trame-server	`3.12.4`	indirect
PyPI	trame-vtk	`2.11.8`	indirect
PyPI	trame-vuetify	`3.2.2`	indirect
PyPI	types-openpyxl	`3.1.5.20260807`	indirect
PyPI	types-pytz	`2026.2.0.20260518`	indirect
PyPI	types-pyyaml	`6.0.12.20260815`	indirect
PyPI	types-sqlalchemy	`1.4.53.38`	indirect
PyPI	typing-extensions	`4.15.0`	indirect
PyPI	typing-inspection	`0.4.2`	indirect
PyPI	tzdata	`2026.2`	indirect
PyPI	ujson	`5.13.0`	indirect
PyPI	urllib3	`2.7.0`	indirect
PyPI	uvicorn	`0.47.0`	indirect
PyPI	virtualenv	`21.3.3`	indirect
PyPI	vtk	`9.6.2`	indirect
PyPI	waitress	`3.0.2`	indirect
PyPI	watchdog	`6.0.0`	indirect
PyPI	watchfiles	`1.2.0`	indirect
PyPI	wcwidth	`0.7.0`	indirect
PyPI	webencodings	`0.5.1`	indirect
PyPI	webob	`1.8.11`	indirect
PyPI	websockets	`16.0`	indirect
PyPI	webtest	`3.0.7`	indirect
PyPI	wheel	`0.47.0`	indirect
PyPI	widgetsnbextension	`4.0.15`	indirect
PyPI	wrapt	`2.2.1`	indirect
PyPI	wslink	`2.5.7`	indirect
PyPI	xarray	`2026.4.0`	indirect
PyPI	xlrd	`2.0.2`	indirect
PyPI	xmlschema	`4.3.1`	indirect
PyPI	xsdata	`26.2`	indirect
PyPI	yarl	`1.24.2`	indirect
PyPI	zarr	`2.18.3`	indirect
PyPI	zarr	`3.1.6`	indirect
PyPI	zict	`3.0.0`	indirect
PyPI	zipp	`4.1.0`	indirect

Dependency advisories 0

Installing pypi:pycytominer@1.7.1 pulls in 21 packages, direct and transitive: 0 carry known advisories, of which 0 are direct dependencies.

No known advisories affect the assessed dependencies.

An advisory means the version recorded in the dependency graph falls inside an advisory’s affected range. Reachability is not analysed, and the graph includes development and test pins — a finding may concern tooling rather than shipped software.

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Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.

Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v2.10.0, schema v0.34.0 — full methodology · metrics wiki.

How one result sits in the wider record: aggregate statistics — PyPI.

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