Public recordExcellent
Software health reportschema 0.14.0 · metrics 2.10.0 · 2026-07-19 01:06 UTC
computational-cell-analytics / micro-sam
Segment Anything for Microscopy
computational-cell-analytics/micro-sam holds a health index of 84 out of 100, placing it in the Excellent band. It scores highest on Vitality (92/100) and lowest on AI Readiness (34/100). It was last updated 1 day ago. A single contributor accounts for most of its recent work.
84
overall / 100Software 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.
84
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 71 is calibrated to 84 on the published index scale (record calibration 2026-08-02).
Ownership
computational-cell-analyticsOrganization
86 followers36 public repossince Jun 2022
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 | micro_sam | 1.8.6 | - | 7 | 1 day ago |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
92
Development activity
87Excellent
How it's scored
| 36/36 | Push recency — last push 1 days ago |
| 22.8/36 | Commit cadence — 33/52 weeks with commits |
| 18/18 | Commit volume — 157 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 21 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 157 |
| human_commit_share | — |
| days_since_last_push | 1 |
| active_weeks_last_year | 33 |
Release discipline
100Exceptional
How it's scored
| 27/27 | Ships releases — 48 releases published |
| 36/36 | Release recency — latest release 1 days ago |
| 27/27 | Release cadence — a release every ~15.5 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 48 |
| latest_release_tag | v1.8.6 |
| releases_from_tags | no |
| days_since_latest_release | 1 |
| mean_days_between_releases | 15.5 |
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?
60
Popularity & adoption
68Good
How it's scored
| 46.2/60 | Stars — 701 stars |
| 16.8/25 | Forks — 105 forks |
| 5/15 | Watchers — 9 watchers |
Inputs used
| forks | 105 |
| stars | 701 |
| watchers | 9 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
50Moderate
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (MIT) |
| 0/18 | CONTRIBUTING guide |
| 0/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 0/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| readme_badges | — |
| has_contributing | no |
| has_issue_template | no |
| has_code_of_conduct | no |
| readme_badge_services | — |
| has_pull_request_template | no |
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
73
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 9.1/22.5 | Commit distribution — top contributor authored 60% of commits |
| 13.5/13.5 | Contributor breadth — 20 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 5 contributing companies or organizations |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 20 |
| top_contributor_share | 0.597 |
Issue & PR responsiveness
81Excellent
How it's scored
| 36.4/42 | Issue resolution — 87% of issues closed |
| 27.8/30 | PR acceptance — 827/892 decided PRs merged |
| 0/13 | Newcomer PR acceptance — no first-time contributor's PR decided in 30d |
| 6/15 | OpenSSF Scorecard: Code-Review — Found 13/27 approved changesets -- score normalized to 4 |
Inputs used
| merged_prs | 827 |
| open_issues | 52 |
| closed_issues | 336 |
| prs_merged_7d | — |
| prs_decided_7d | — |
| prs_merged_30d | — |
| prs_decided_30d | — |
| issue_closed_ratio | 0.866 |
| closed_unmerged_prs | 65 |
| first_time_authors_30d | — |
| first_time_prs_merged_30d | — |
| first_time_prs_decided_30d | — |
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.
Ownership & stewardship
80Excellent
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain — verified-domain status not read for this organization |
| 13.9/25 | Owner reach — 86 followers of computational-cell-analytics |
| 19.7/25 | Track record — 36 public repos, account ~4 yr old |
Inputs used
| followers | 86 |
| owner_type | Organization |
| is_verified | — |
| owner_login | computational-cell-analytics |
| public_repos | 36 |
| account_age_days | 1,508 |
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.
Package maintenance
100Exceptional
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 1 days ago |
| 20/20 | Version history — 7 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | micro_sam |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 1 |
Engineering Quality
Are baseline engineering and documentation practices in place?
77
Engineering practices
68Good
How it's scored
| 24/24 | CI workflows — 6 workflow(s) |
| 24/24 | Tests present |
| 0/16 | Linter config |
| 0/9.6 | 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 | no |
| has_precommit_config | no |
Documentation
90Excellent
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://computational-cell-analytics.github.io/micro-sam/ |
| 10/10 | Repository description |
| 10/10 | Topics — 9 topics |
| 0/10 | Wiki |
Inputs used
| topics | microscopy-images, segment-anything, segmentation, cell-segmentation, napari, nuclei-segmentation, mitochondria-segmentation, micro-sam, bioimage-analysis |
| has_wiki | no |
| homepage | https://computational-cell-analytics.github.io/micro-sam/ |
| docs_site | https://computational-cell-analytics.github.io/micro-sam/ |
| 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?
53
Security posture
53Moderate
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 |
| 3/7.5 | Code-Review — Found 13/27 approved changesets -- score normalized to 4 |
| 2.5/2.5 | Contributors — project has 5 contributing companies or organizations |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 0/7.5 | Dependency-Update-Tool — no 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 21 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 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — no data |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 16 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 2 |
| scorecard_aggregate | 5.3 |
Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.
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.
34
Agent context & guidance
1Critical
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 0/40 | Legible commit history — no data |
Inputs used
| has_llms_txt | no |
| llms_txt_url | — |
| legible_history_share | — |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.
How it's scored
| 0/18 | One-command bootstrap |
| 22/22 | Automated tests |
| 0/11 | Lint / format config |
| 0/11 | Static type checking |
| 0/10 | Reproducible environment |
| 0/10 | Demonstrated agent practice — no data |
| 0/8 | Automated maintenance — no data |
| 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 | — |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | — |
| has_devcontainer | no |
| has_linter_config | no |
| typecheck_configs | — |
| agent_commit_share | — |
| toolchain_manifests | — |
| dependency_bot_commit_share | — |
Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.
Code legibility for models
54Moderate
How it's scored
| 0/45 | Type-checkable code — Jupyter Notebook without a type-check config |
| 54.3/55 | Manageable file sizes — 3/247 source files over 60KB |
Inputs used
| primary_language | Jupyter Notebook |
| largest_source_bytes | 87,623 |
| source_files_sampled | 247 |
| oversized_source_files | 3 |
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 — examples, notebooks |
Inputs used
| example_dirs | examples, 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
701GitHub stars
20contributors
157commits, last 12 months
1days since last push
48releases
1bus factor
52open issues
PyPIpackage ecosystems
More detail
OpenSSF Scorecard 5.3 / 10
5.3aggregate
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).
| 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 |
| 4 | Code-Review | Found 13/27 approved changesets -- score normalized to 4 |
| 10 | Contributors | project has 5 contributing companies or organizations |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 21 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 |
| 0 | Security-Policy | security policy file not detected |
| n/a | Signed-Releases | no releases found |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 30
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | bioimage-cpp | >=0.3 | setup.cfg |
| PyPI | bioimageio.core | — | setup.cfg |
| PyPI | h5py | — | setup.cfg |
| PyPI | imagecodecs | — | setup.cfg |
| PyPI | imageio | — | setup.cfg |
| PyPI | joblib | — | setup.cfg |
| PyPI | kornia | — | setup.cfg |
| PyPI | magicgui | — | setup.cfg |
| PyPI | matplotlib | — | setup.cfg |
| PyPI | napari | >=0.7 | setup.cfg |
| PyPI | natsort | — | setup.cfg |
| PyPI | networkx | — | setup.cfg |
| PyPI | numpy | — | setup.cfg |
| PyPI | pandas | — | setup.cfg |
| PyPI | pooch | — | setup.cfg |
| PyPI | PyQt6 | — | setup.cfg |
| PyPI | python-elf | >=0.9 | setup.cfg |
| PyPI | scikit-image | — | setup.cfg |
| PyPI | scikit-learn | — | setup.cfg |
| PyPI | segment-anything | — | setup.cfg |
| PyPI | superqt | — | setup.cfg |
| PyPI | timm | — | setup.cfg |
| PyPI | torch | >=2.5 | setup.cfg |
| PyPI | torch-em | >=0.9 | setup.cfg |
| PyPI | torchvision | — | setup.cfg |
| PyPI | tqdm | — | setup.cfg |
| PyPI | trackastra | >=0.5.3 | setup.cfg |
| PyPI | xarray | — | setup.cfg |
| PyPI | xxhash | — | setup.cfg |
| PyPI | zarr | — | setup.cfg |
All dependencies 41
Full resolved dependency set from the GitHub dependency graph: 30 direct and 11 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | bioimage-cpp | — | direct |
| PyPI | bioimageio-core | — | direct |
| PyPI | h5py | — | direct |
| PyPI | imagecodecs | — | direct |
| PyPI | imageio | — | direct |
| PyPI | joblib | — | direct |
| PyPI | kornia | — | direct |
| PyPI | magicgui | — | direct |
| PyPI | matplotlib | — | direct |
| PyPI | napari | — | direct |
| PyPI | natsort | — | direct |
| PyPI | networkx | — | direct |
| PyPI | numpy | — | direct |
| PyPI | pandas | — | direct |
| PyPI | pooch | — | direct |
| PyPI | pyqt6 | — | direct |
| PyPI | python-elf | — | direct |
| PyPI | scikit-image | — | direct |
| PyPI | scikit-learn | — | direct |
| PyPI | segment-anything | — | direct |
| PyPI | superqt | — | direct |
| PyPI | timm | — | direct |
| PyPI | torch | — | direct |
| PyPI | torch-em | — | direct |
| PyPI | torchvision | — | direct |
| PyPI | tqdm | — | direct |
| PyPI | trackastra | — | direct |
| PyPI | xarray | — | direct |
| PyPI | xxhash | — | direct |
| PyPI | zarr | — | direct |
| PyPI | build | — | indirect |
| PyPI | coverage | — | indirect |
| PyPI | line-profiler | — | indirect |
| PyPI | pdoc | — | indirect |
| PyPI | pytest | — | indirect |
| PyPI | pytest-cov | — | indirect |
| PyPI | pytest-qt | — | indirect |
| PyPI | setuptools | — | indirect |
| PyPI | snakeviz | — | indirect |
| PyPI | tabulate | — | indirect |
| PyPI | twine | — | indirect |
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.
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 v0.14.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.