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Open Source Science

https://github.com/alleninstitute/em_stitch

EM microscopy lens correction

https://github.com/alleninstitute/em_stitch

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 6 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

EM microscopy lens correction

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: bsd-2-clause
  • Language: Python
  • Default Branch: master
  • Size: 86.4 MB
Statistics
  • Stars: 4
  • Watchers: 7
  • Forks: 3
  • Open Issues: 3
  • Releases: 5
Created over 7 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Contributing License

README.md

Build Status codecov

em_stitch

Lens correction solver and stitching utilities for EM images.

This repo has overlap with https://github.com/AllenInstitute/asap-modules

It is meant to be independent of asap-modules and a running render server.

Installation

This package is pip-installable with pip install em-stitch

installing from this repo can be accomplished with python setup.py install

Optional dependencies

The performance of em-stitch can benefit from the installation of pandas and will use it when available. Bigfeta will use petsc4py to implement its solver if available, which can improve memory utilization and performance.

support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests. Please make pull requests against the develop branch, as we will test changes there before merging into master.

Acknowledgement of Government Sponsorship

Supported by the Intelligence Advanced Research Projects Activity (IARPA) via Department of Interior / Interior Business Center (DoI/IBC) contract number D16PC00004. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation thereon. Disclaimer: The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of IARPA, DoI/IBC, or the U.S. Government.

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Issues event: 4
  • Issue comment event: 1
Last Year
  • Issues event: 4
  • Issue comment event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 175
  • Total Committers: 6
  • Avg Commits per committer: 29.167
  • Development Distribution Score (DDS): 0.286
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Dan Kapner d****k@.****g 125
Russel Torres r****s@g****m 27
Dan Kapner 3****r 16
Jay Borseth j****b@a****g 5
jayb j****h@h****m 1
dlbrittain d****n@g****m 1
Committer Domains (Top 20 + Academic)
alleninstitute.org: 1 .alleninstitute.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 6
  • Total pull requests: 54
  • Average time to close issues: almost 2 years
  • Average time to close pull requests: 5 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.67
  • Average comments per pull request: 1.04
  • Merged pull requests: 53
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • RussTorres (4)
  • djkapner (1)
  • ghost (1)
Pull Request Authors
  • djkapner (41)
  • RussTorres (15)
  • dlbrittain (1)
Top Labels
Issue Labels
help wanted (1) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 21 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 15
  • Total maintainers: 2
pypi.org: em-stitch

a python package for stitching EM images

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 21 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 16.8%
Average: 18.8%
Dependent repos count: 21.6%
Downloads: 22.6%
Stargazers count: 23.1%
Maintainers (2)
djkapner RussTorres
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • argschema <2.0
  • bigfeta >=1.0.3
  • marshmallow <3.0
  • numpy >=1.13
  • opencv-python *
  • render-python >=2.2.0
  • scipy >=1.2.1
  • triangle *
test_requirements.txt pypi
  • coverage >=4.1 test
  • flake8 >=3.0.4 test
  • jinja2 * test
  • mccabe <0.7.0,>=0.6.0 test
  • mock >=2.0.0 test
  • pep8 >=1.7.0 test
  • pylint >=1.5.4 test
  • pytest >=3.0.5 test
  • pytest-cov >=2.2.1 test
  • pytest-pep8 >=1.0.6 test
  • pytest-xdist >=1.14 test
  • scikit-image * test
  • shapely * test
.github/workflows/release_publish.yml actions
  • actions/checkout v2 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/tests.yml actions
  • EnricoMi/publish-unit-test-result-action v1 composite
  • actions/checkout v2 composite
  • actions/download-artifact v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
  • codecov/codecov-action v2 composite
setup.py pypi