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cylinter

An Interactive Image Segmentation Filter for Multiplex Microscopy

https://github.com/labsyspharm/cylinter

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

An Interactive Image Segmentation Filter for Multiplex Microscopy

Basic Info
Statistics
  • Stars: 31
  • Watchers: 2
  • Forks: 13
  • Open Issues: 4
  • Releases: 13
Created almost 6 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

An Interactive Image Segmentation Filter for Multiplex Microscopy.

CyLinter is quality control software for identifying and removing cell segmentation instances corrupted by optical and/or image-processing artifacts in multiplex microscopy images. The tool is interactive and comprises a set of modular and extensible QC modules instantiated in a configurable Python Class object. Module results are cached to allow for progress bookmarking and dynamic restarts.

CyLinter development is led by Greg Baker at the Laboratory of Systems Pharmacology, Harvard Medical School.

Funding: This work was supported by the Ludwig Cancer Research and the Ludwig Center at Harvard (P.K.S., S.S.) and by NIH NCI grants U2C-CA233280, and U2C-CA233262 (P.K.S., S.S.). Development of computational methods and image processing software is supported by a Team Science Grant from the Gray Foundation (P.K.S., S.S.), the Gates Foundation grant INV-027106 (P.K.S.), the David Liposarcoma Research Initiative at Dana-Farber Cancer Institute supported by KBF Canada via the Rossy Foundation Fund (P.K.S., S.S.) and the Emerson Collective (P.K.S.). S.S. is supported by the BWH Presidents Scholars Award.

Project Website: https://labsyspharm.github.io/cylinter/

Owner

  • Name: Laboratory of Systems Pharmacology @ Harvard
  • Login: labsyspharm
  • Kind: organization
  • Email: hits@harvard.edu
  • Location: Boston, MA

Reinventing the fundamental science underlying the development of new medicines and their use in individual patients.

GitHub Events

Total
  • Create event: 7
  • Release event: 5
  • Issues event: 13
  • Watch event: 8
  • Delete event: 6
  • Issue comment event: 24
  • Push event: 11
  • Pull request event: 23
  • Fork event: 2
Last Year
  • Create event: 7
  • Release event: 5
  • Issues event: 13
  • Watch event: 8
  • Delete event: 6
  • Issue comment event: 24
  • Push event: 11
  • Pull request event: 23
  • Fork event: 2

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 171
  • Total Committers: 4
  • Avg Commits per committer: 42.75
  • Development Distribution Score (DDS): 0.047
Top Committers
Name Email Commits
gjbaker g****2@h****u 163
Yu-An Chen a****2@g****m 4
Jeremy Muhlich j****h@b****g 2
Hung-Yi Wu 1****u@u****m 2
Committer Domains (Top 20 + Academic)
bitflood.org: 1 hms.harvard.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 22
  • Total pull requests: 174
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 16
  • Total pull request authors: 6
  • Average comments per issue: 2.73
  • Average comments per pull request: 0.02
  • Merged pull requests: 165
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 9
  • Pull requests: 19
  • Average time to close issues: 6 days
  • Average time to close pull requests: less than a minute
  • Issue authors: 8
  • Pull request authors: 1
  • Average comments per issue: 0.56
  • Average comments per pull request: 0.0
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • josenimo (6)
  • emir-radkevich (2)
  • DarioS (1)
  • saikatds-bd (1)
  • MDHowe4 (1)
  • ChiaraCaprioli (1)
  • MahiruTrejo55 (1)
  • fotisn7 (1)
  • aandytu (1)
  • charles-xue (1)
  • psenin-sanofi (1)
  • kimnguyen72 (1)
  • FloWuenne (1)
  • adajnq (1)
  • jmuhlich (1)
Pull Request Authors
  • gjbaker (164)
  • ziyuanzhao2000 (4)
  • jmuhlich (3)
  • ArtemSokolov (1)
  • Yu-AnChen (1)
  • dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 989 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 54
  • Total maintainers: 2
proxy.golang.org: github.com/labsyspharm/cylinter
  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 6.5%
Average: 6.7%
Dependent repos count: 7.0%
Last synced: 10 months ago
pypi.org: cylinter

CyLinter

  • Versions: 45
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 989 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 10.9%
Stargazers count: 13.3%
Average: 14.2%
Downloads: 15.2%
Dependent repos count: 21.6%
Maintainers (2)
gjbaker jmuhlich
Last synced: 10 months ago