Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-10-19 11:10 UTC

PixelgenTechnologies / pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

PythonMIT★ 22 stars⑂ 6 forkssince Sep 2023View on GitHub ↗
KindCommand-line toolLibraryhow this is determined

PixelgenTechnologies/pixelator holds a health index of 92 out of 100, placing it in the Excellent band. It scores highest on Engineering Quality (100/100) and lowest on Community & Adoption (48/100). It was last updated today. 2 contributors account for most of its recent work.

92
overall / 100
Excellent

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.

92
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)
VitalityCommunity &AdoptionSustainability &GovernanceEngineeringQualitySecurityAI Readiness

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 78 is calibrated to 92 on the published index scale (record calibration 2026-08-02).

Ownership

26 followers15 public repossince Oct 2020

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIpixelgen-pixelator0.30.01693775 days agomolecular-pixelationproteinproteomicssingle-cellspatial

Metrics by category

Vitality

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

96Exceptional · 21% of overall
How it's scored
36/36Push recency — last push 0 days ago
29.8/36Commit cadence — 43/52 weeks with commits
18/18Commit volume — 739 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year739
human_commit_share0.98
days_since_last_push0
active_weeks_last_year43

Release discipline

100Exceptional
How it's scored
27/27Ships releases — 38 releases published
36/36Release recency — latest release 75 days ago
27/27Release cadence — a release every ~27.4 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count38
latest_release_tagv0.30.0
releases_from_tagsno
days_since_latest_release75
mean_days_between_releases27.4
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?

48Weak · 17% of overall
How it's scored
21.4/60Stars — 22 stars
5.8/25Forks — 6 forks
2.7/15Watchers — 4 watchers
Inputs used
forks6
stars22
watchers4
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (MIT)
18/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
6.3/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges5
has_contributingyes
has_issue_templateno
has_code_of_conductno
readme_badge_servicesgithub.com, shields.io
has_pull_request_templateyes
How it's scored
29.7/80Monthly downloads — 169 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packagespixelgen-pixelator
dependents—
ecosystemspypi
total_downloads—
monthly_downloads169
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?

76Good · 23% of overall
How it's scored
25.2/54Bus factor — 2 contributor(s) cover half of all commits
15/22.5Commit distribution — top contributor authored 33% of commits
13.5/13.5Contributor breadth — 13 contributors
10/10OpenSSF Scorecard: Contributors — project has 6 contributing companies or organizations
Inputs used
bus_factor2
contributors_sampled13
top_contributor_share0.334
How it's scored
42/42Issue resolution — 100% of issues closed
26.7/30PR acceptance — 444/498 decided PRs merged
6.5/13Newcomer PR acceptance — 1/2 first-time contributors' PRs merged in 30d
10.5/15OpenSSF Scorecard: Code-Review — Found 15/20 approved changesets -- score normalized to 7
Inputs used
merged_prs444
open_issues0
closed_issues1
prs_merged_7d11
prs_decided_7d18
prs_merged_30d24
prs_decided_30d34
issue_closed_ratio1
closed_unmerged_prs54
first_time_authors_30d1
first_time_prs_merged_30d1
first_time_prs_decided_30d2
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
10.3/25Owner reach — 26 followers of PixelgenTechnologies
20.8/25Track record — 15 public repos, account ~6 yr old
Inputs used
followers26
owner_typeOrganization
is_verifiedno
owner_loginPixelgenTechnologies
public_repos15
account_age_days2,193

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 75 days ago
20/20Version history — 37 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagespixelgen-pixelator
ecosystemspypi
any_deprecatedno
min_days_since_publish75

Engineering Quality

Are baseline engineering and documentation practices in place?

100Exceptional · 19% of overall

Engineering practices

100Exceptional
How it's scored
24/24CI workflows — 6 workflow(s)
24/24Tests present
16/16Linter config — pyproject.toml ([tool.ruff])
9.6/9.6Pre-commit hooks
6.4/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 20 out of 20 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigyes
has_linter_configyes
has_precommit_configyes

Documentation

100Exceptional
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — https://pixelgen.com
10/10Repository description
10/10Topics — 8 topics
10/10Wiki
Inputs used
topicsmolecular-pixelation, pixelgen-technologies, protein, proteomics, single-cell, single-cell-omics, spatial, proximity-network
has_wikiyes
homepagehttps://pixelgen.com
docs_sitehttps://pixelgen.com
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

68Good · 16% of overall
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0.8/7.5Branch-Protection — branch protection is not maximal on development and all release branches
2.5/2.5CI-Tests — 20 out of 20 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
5.2/7.5Code-Review — Found 15/20 approved changesets -- score normalized to 7
2.5/2.5Contributors — project has 6 contributing companies or organizations
10/10Dangerous-Workflow — no dangerous workflow patterns detected
7.5/7.5Dependency-Update-Tool — update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — license file detected
7.5/7.5Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
5/5Packaging — packaging workflow detected
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — no data
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated17
scorecard_versionv5.5.0
checks_inconclusive1
scorecard_aggregate6
Excluded from scoring (no data or not applicable): Signed-Releases. Remaining weights renormalized.

Dependency advisories

100Exceptional
How it's scored
35/35Direct dependencies free of known advisories — no direct dependency carries a known advisory
25/25Indirect dependencies free of known advisories — no indirect dependency carries a known advisory
0/40No advisories left outstanding — no advisory carries a publication date
Inputs used
sourceosv
advisories0
affected_packages0
assessed_packages83
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:pixelgen-pixelator@0.30.0 runtime dependency closure — what installing the published package pulls in — 83 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.

59Moderate · 4% of overall
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
32.7/40Legible commit history — 60 of 98 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share0.612
agent_instruction_files—
agent_instruction_max_bytes—
How it's scored
18/18One-command bootstrap — Taskfile.yml, docs/Makefile, tests/Taskfile.yml
22/22Automated tests
11/11Lint / format config — pyproject.toml ([tool.ruff])
0/11Static type checking
10/10Reproducible environment — lockfile
10/10Demonstrated agent practice — 15 of the last 100 commits agent-authored or agent-credited
8/8Automated maintenance — 2 of the last 100 commits are automated dependency updates
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilesuv.lock
has_dockerfileno
typed_languageno
bootstrap_filesTaskfile.yml, docs/Makefile, tests/Taskfile.yml
has_devcontainerno
has_linter_configyes
typecheck_configs—
agent_commit_share0.15
toolchain_manifests—
dependency_bot_commit_share0.02
How it's scored
0/45Type-checkable code — Python without a type-check config
55/55Manageable file sizes — 0/295 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes54,625
source_files_sampled295
oversized_source_files0

Key facts

22GitHub stars
13contributors
739commits, last 12 months
0days since last push
38releases
2bus factor
0open 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 ★ / 6 ⇿
0Stars
6Forks
36Releases

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.

123456612023-092025-042026-10
Major 0Minor 17Patch 19

Each point covers 3 days.

OpenSSF Scorecard 6.0 / 10
6.0aggregate

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 · 2026-10-19 11:09 UTC

10Binary-Artifactsno binaries found in the repo
1Branch-Protectionbranch protection is not maximal on development and all release branches
10CI-Tests20 out of 20 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
7Code-ReviewFound 15/20 approved changesets -- score normalized to 7
10Contributorsproject has 6 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
10Packagingpackaging workflow detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
10Vulnerabilities0 existing vulnerabilities detected
Direct dependencies 28
RegistryPackageVersion constraintManifest
PyPIclick<8.3pyproject.toml
PyPIcutadapt>=4.2pyproject.toml
PyPIxopen—pyproject.toml
PyPIpyfastx—pyproject.toml
PyPIyappi—pyproject.toml
PyPIpandas>=2.0.0,<3.0.0pyproject.toml
PyPInumpy>=2.0.0,<3.0.0pyproject.toml
PyPIannoy<=1.17.0pyproject.toml
PyPIxxhash—pyproject.toml
PyPIanndata>=0.8.0pyproject.toml
PyPInumba>=0.56.4pyproject.toml
PyPIscanpy—pyproject.toml
PyPItyping_extensions—pyproject.toml
PyPIscipy>=1.11.0,<2.0.0pyproject.toml
PyPIpyarrow>=14pyproject.toml
PyPIsemver>=3.0.0,<4pyproject.toml
PyPIruamel-yaml>=0.17.21,<0.18pyproject.toml
PyPIpydantic>=2.12.4,<3.0pyproject.toml
PyPIpolars>=1.0.0,<2.0.0pyproject.toml
PyPIimportlib-resources>=5.12.0,<6pyproject.toml
PyPIfsspec—pyproject.toml
PyPIplotly—pyproject.toml
PyPIgraspologic-native>=1.2.4,<2pyproject.toml
PyPIduckdb>=1.4.2,<2pyproject.toml
PyPIfaiss-cpu>=1.10.0,<2pyproject.toml
PyPIlevenshtein>=0.27.3pyproject.toml
PyPIpixelgen-pixelator-core>=0.2.0,<0.3pyproject.toml
PyPIrequests>=2.32.5pyproject.toml
All dependencies 186

Full resolved dependency set from the GitHub dependency graph: 33 direct and 153 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIanndata0.11.4direct
PyPIanndata0.12.18direct
PyPIannoy1.17.0direct
PyPIclick8.2.1direct
PyPIcutadapt5.2direct
PyPIduckdb1.5.4direct
PyPIfaiss-cpu1.14.3direct
PyPIfsspec2026.6.0direct
PyPIgraspologic-native1.3.1direct
PyPIimportlib-resources5.13.0direct
PyPIlevenshtein0.27.3direct
PyPInumba0.65.1direct
PyPInumpy2.2.6direct
PyPInumpy2.4.6direct
PyPIpandas2.3.3direct
PyPIpixelgen-pixelator-core0.2.0direct
PyPIplotly6.8.0direct
PyPIpolars1.42.1direct
PyPIpyarrow24.0.0direct
PyPIpydantic2.13.4direct
PyPIpyfastx2.3.1direct
PyPIrequests2.34.2direct
PyPIruamel-yaml0.17.40direct
PyPIscanpy1.11.5direct
PyPIscanpy1.12.2direct
PyPIscipy1.15.3direct
PyPIscipy1.17.1direct
PyPIscipy1.18.0direct
PyPIsemver3.0.4direct
PyPItyping-extensions4.15.0direct
PyPIxopen2.1.0direct
PyPIxxhash3.8.0direct
PyPIyappi1.7.6direct
PyPIaccessible-pygments0.0.5indirect
PyPIalabaster1.0.0indirect
PyPIannotated-types0.7.0indirect
PyPIanyio4.14.2indirect
PyPIappnope0.1.4indirect
PyPIarray-api-compat1.15.0indirect
PyPIast-serialize0.6.0indirect
PyPIastroid4.1.2indirect
PyPIasttokens3.0.1indirect
PyPIbabel2.18.0indirect
PyPIbackports-zstd1.6.0indirect
PyPIbeautifulsoup44.15.0indirect
PyPIcertifi2026.6.17indirect
PyPIcffi2.0.0indirect
PyPIcfgv3.5.0indirect
PyPIcharset-normalizer3.4.7indirect
PyPIcolorama0.4.6indirect
PyPIcomm0.2.3indirect
PyPIcontourpy1.3.2indirect
PyPIcontourpy1.3.3indirect
PyPIcoverage7.14.3indirect
PyPIcycler0.12.1indirect
PyPIdebugpy1.8.21indirect
PyPIdecorator5.3.1indirect
PyPIdistlib0.4.3indirect
PyPIdnaio1.2.4indirect
PyPIdocutils0.21.2indirect
PyPIdocutils0.22.4indirect
PyPIdonfig0.8.1.post1indirect
PyPIexceptiongroup1.3.1indirect
PyPIexecuting2.2.1indirect
PyPIfast-array-utils1.4.1indirect
PyPIfilelock3.29.4indirect
PyPIfonttools4.63.0indirect
PyPIgoogle-crc32c1.8.0indirect
PyPIh110.16.0indirect
PyPIh5py3.16.0indirect
PyPIidentify2.6.19indirect
PyPIidna3.18indirect
PyPIimagesize2.0.0indirect
PyPIiniconfig2.3.0indirect
PyPIinvoke3.0.3indirect
PyPIipykernel7.3.0indirect
PyPIipython8.39.0indirect
PyPIipython9.15.0indirect
PyPIipython-pygments-lexers1.1.1indirect
PyPIisal1.8.0indirect
PyPIisort8.0.1indirect
PyPIjedi0.20.0indirect
PyPIjinja23.1.6indirect
PyPIjoblib1.5.3indirect
PyPIjupyter-client8.9.1indirect
PyPIjupyter-core5.9.1indirect
PyPIkiwisolver1.5.0indirect
PyPIlegacy-api-wrap1.5indirect
PyPIlibrt0.12.0indirect
PyPIline-profiler5.0.2indirect
PyPIllvmlite0.47.0indirect
PyPImarkupsafe3.0.3indirect
PyPImatplotlib3.10.9indirect
PyPImatplotlib-inline0.2.2indirect
PyPImypy2.1.0indirect
PyPImypy-extensions1.1.0indirect
PyPInarwhals2.23.0indirect
PyPInatsort8.4.0indirect
PyPInest-asyncio21.7.2indirect
PyPInetworkx3.4.2indirect
PyPInetworkx3.6.1indirect
PyPInodeenv1.10.0indirect
PyPInumcodecs0.16.5indirect
PyPIpackaging26.2indirect
PyPIparso0.8.7indirect
PyPIpathspec1.1.1indirect
PyPIpatsy1.0.2indirect
PyPIpexpect4.9.0indirect
PyPIpillow12.3.0indirect
PyPIplatformdirs4.10.0indirect
PyPIpluggy1.6.0indirect
PyPIpolars-runtime-321.42.1indirect
PyPIpre-commit4.6.0indirect
PyPIprompt-toolkit3.0.52indirect
PyPIpsutil7.2.2indirect
PyPIptyprocess0.7.0indirect
PyPIpure-eval0.2.3indirect
PyPIpy-cpuinfo9.0.0indirect
PyPIpycparser3.0indirect
PyPIpydantic-core2.46.4indirect
PyPIpydata-sphinx-theme0.19.0indirect
PyPIpygments2.20.0indirect
PyPIpynndescent0.6.0indirect
PyPIpyparsing3.3.2indirect
PyPIpytest9.1.1indirect
PyPIpytest-benchmark5.2.3indirect
PyPIpytest-cov7.1.0indirect
PyPIpytest-mock3.15.1indirect
PyPIpytest-mpl0.19.0indirect
PyPIpytest-snapshot0.9.0indirect
PyPIpytest-watcher0.6.3indirect
PyPIpython-dateutil2.9.0.post0indirect
PyPIpython-discovery1.6.1indirect
PyPIpytz2026.2indirect
PyPIpyyaml6.0.3indirect
PyPIpyzmq27.1.0indirect
PyPIrapidfuzz3.14.5indirect
PyPIroman-numerals4.1.0indirect
PyPIruamel-yaml-clib0.2.15indirect
PyPIruff0.15.20indirect
PyPIscikit-learn1.7.2indirect
PyPIscikit-learn1.9.0indirect
PyPIscverse-misc0.0.3indirect
PyPIscverse-misc0.1.1indirect
PyPIseaborn0.13.2indirect
PyPIsession-info20.4.1indirect
PyPIsix1.17.0indirect
PyPIsnowballstemmer3.1.1indirect
PyPIsoupsieve2.9indirect
PyPIsphinx8.1.3indirect
PyPIsphinx9.0.4indirect
PyPIsphinx9.1.0indirect
PyPIsphinx-autoapi3.8.0indirect
PyPIsphinx-autobuild2024.10.3indirect
PyPIsphinx-autobuild2025.8.25indirect
PyPIsphinx-click6.2.0indirect
PyPIsphinx-design0.6.1indirect
PyPIsphinx-design0.7.0indirect
PyPIsphinxcontrib-applehelp2.0.0indirect
PyPIsphinxcontrib-devhelp2.0.0indirect
PyPIsphinxcontrib-htmlhelp2.1.0indirect
PyPIsphinxcontrib-jsmath1.0.1indirect
PyPIsphinxcontrib-qthelp2.0.0indirect
PyPIsphinxcontrib-serializinghtml2.0.0indirect
PyPIstack-data0.6.3indirect
PyPIstarlette1.3.1indirect
PyPIstatsmodels0.14.6indirect
PyPIthreadpoolctl3.6.0indirect
PyPItomli2.4.1indirect
PyPItornado6.5.9indirect
PyPItqdm4.68.3indirect
PyPItraitlets5.15.1indirect
PyPItypes-requests2.33.0.20260518indirect
PyPItyping-inspection0.4.2indirect
PyPItzdata2026.2indirect
PyPIumap-learn0.5.12indirect
PyPIurllib32.8.0indirect
PyPIuvicorn0.49.0indirect
PyPIvirtualenv21.7.13indirect
PyPIwatchdog6.0.0indirect
PyPIwatchfiles1.2.0indirect
PyPIwcwidth0.8.2indirect
PyPIwebsockets16.0indirect
PyPIzarr3.1.6indirect
PyPIzarr3.2.1indirect
PyPIzlib-ng1.0.0indirect
Dependency advisories 0

Installing pypi:pixelgen-pixelator@0.30.0 pulls in 83 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.

Raw JSON report machine-readable

Feedback

Spotted something off in this report, or have thoughts to share? Wrong measurements, missed tooling, ideas, questions — anything is welcome. Every message is read and gets a response.

The message is kept through sign-in.

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.