https://github.com/biigle/maia

:m: BIIGLE module for the Machine Learning Assisted Image Annotation method

Science Score: 39.0%

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Low similarity (12.6%) to scientific vocabulary

Keywords

biigle biigle-module

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Last synced: 10 months ago · JSON representation

Repository

:m: BIIGLE module for the Machine Learning Assisted Image Annotation method

Basic Info

Host: GitHub
Owner: biigle
License: gpl-3.0
Language: PHP
Default Branch: master
Homepage:
Size: 5 MB

Statistics

Stars: 2
Watchers: 2
Forks: 3
Open Issues: 46
Releases: 108

Topics

biigle biigle-module

Created about 8 years ago · Last pushed 10 months ago

Metadata Files

Readme License

BIIGLE MAIA Module

This is the BIIGLE module module for the Machine Learning Assisted Image Annotation method.

Installation

Run composer require biigle/maia.
Install the Python dependencies with pip install -r requirements.txt.
Add Biigle\Modules\Maia\MaiaServiceProvider::class to the providers array in config/app.php.
Run php artisan vendor:publish --tag=public to publish the public assets of this module.
Run docker-compose exec app php artisan migrate to create the new database tables.
Configure a storage disk each for the training proposal and annotation candidate patches. Set the MAIA_TRAINING_PROPOSAL_STORAGE_DISK and MAIA_ANNOTATION_CANDIDATE_STORAGE_DISK variables in the .env file to the name of the respective storage disk. Do not use the same disk for both! The content of the storage disks should be publicly accessible. Example for local disks: php // MAIA_TRAINING_PROPOSAL_STORAGE_DISK 'maia-tp' => [ 'driver' => 'local', 'root' => storage_path('app/public/maia-tp-patches'), 'url' => env('APP_URL').'/storage/maia-tp-patches', 'visibility' => 'public', ], // MAIA_ANNOTATION_CANDIDATE_STORAGE_DISK 'maia-ac' => [ 'driver' => 'local', 'root' => storage_path('app/public/maia-ac-patches'), 'url' => env('APP_URL').'/storage/maia-ac-patches', 'visibility' => 'public', ], This requires the link storage -> ../storage/app/public in the public directory.

Configuration

New processing jobs are submitted to the default queue of the gpu connection. You can configure these with the MAIA_JOB_QUEUE and MAIA_JOB_CONNECTION environment variables. Optionally, you can configure a different queue (but not connection) fot the jobs to generate feature vectors with MAIA_FEATURE_VECTOR_QUEUE. This can be used to give jobs to generate feature vectors a higher priority.

References

Reference publications that you should cite if you use MAIA for one of your studies.

BIIGLE 2.0 Langenkämper, D., Zurowietz, M., Schoening, T., & Nattkemper, T. W. (2017). Biigle 2.0-browsing and annotating large marine image collections. Frontiers in Marine Science, 4, 83. doi: 10.3389/fmars.2017.00083
MAIA Zurowietz, M., Langenkämper, D., Hosking, B., Ruhl, H. A., & Nattkemper, T. W. (2018). MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration. PloS one, 13(11), e0207498. doi: 10.1371/journal.pone.0207498

Developing

Take a look at the development guide of the core repository to get started with the development setup.

Want to develop a new module? Head over to the biigle/module template repository.

Contributions and bug reports

Contributions to BIIGLE are always welcome. Check out the contribution guide to get started.

Owner

Name: BIIGLE
Login: biigle
Kind: organization
Location: Bielefeld University

Website: https://biigle.de
Repositories: 48
Profile: https://github.com/biigle

GitHub Events

Total

Create event: 24
Issues event: 3
Release event: 7
Delete event: 10
Issue comment event: 4
Push event: 24
Pull request event: 29

Last Year

Create event: 24
Issues event: 3
Release event: 7
Delete event: 10
Issue comment event: 4
Push event: 24
Pull request event: 29

Committers

Last synced: over 3 years ago

All Time

Total Commits: 407
Total Committers: 3
Avg Commits per committer: 135.667
Development Distribution Score (DDS): 0.032

Top Committers

Name	Email	Commits
Martin Zurowietz	m**n@z**e	394
dependabot[bot]	4**]@u**m	10
Martin Zurowietz	m**r@u**m	3

Committer Domains (Top 20 + Academic)

zurowietz.de: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 89
Total pull requests: 85
Average time to close issues: 8 months
Average time to close pull requests: 26 days
Total issue authors: 4
Total pull request authors: 4
Average comments per issue: 1.17
Average comments per pull request: 0.25
Merged pull requests: 77
Bot issues: 0
Bot pull requests: 29

Past Year

Issues: 3
Pull requests: 19
Average time to close issues: N/A
Average time to close pull requests: 16 days
Issue authors: 2
Pull request authors: 3
Average comments per issue: 0.33
Average comments per pull request: 0.05
Merged pull requests: 17
Bot issues: 0
Bot pull requests: 7

View more stats

Top Authors

Issue Authors

mzur (77)
dlangenk (9)
charleygros (2)
rvankevelaer (1)

Pull Request Authors

mzur (72)
dependabot[bot] (39)
lehecht (6)
sagunshre (2)

Top Labels

Issue Labels

bug (19) discuss (6)

Pull Request Labels

dependencies (39) javascript (28) python (9)

Packages

Total packages: 1
Total downloads:
- packagist 8,168 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 107
Total maintainers: 1

packagist.org: biigle/maia

BIIGLE module module for the Machine Learning Assisted Image Annotation method.

Homepage: https://biigle.de
License: GPL-3.0-only
Latest release: v2.8.5
published 10 months ago

Versions: 107
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 8,168 Total

Rankings

Forks count: 9.5%

Downloads: 14.4%

Stargazers count: 17.9%

Average: 18.9%

Dependent packages count: 19.1%

Dependent repos count: 33.5%

Maintainers (1)

mzur

Funding

Last synced: 10 months ago

Dependencies

.github/workflows/lint.yml actions

actions/checkout v1 composite

.github/workflows/test.yml actions

actions/checkout v1 composite

package-lock.json npm

803 dependencies

package.json npm

@mzur/laravel-mix-artisan-publish ^1.0.0 development
cross-env ^5.1 development
eslint ^7.3.1 development
eslint-plugin-vue ^7.0.0 development
laravel-mix ^6.0.13 development
resolve-url-loader ^5.0.0 development
sass ^1.15.2 development
sass-loader ^8.0.0 development
vue-loader ^15.9.6 development
vue-template-compiler ^2.6.11 development
ol ^5.3.3

composer.json packagist

biigle/laravel-file-cache ^3.0 || ^4.0
biigle/largo ^2.25 || dev-master

requirements.txt pypi

albumentations *
mmcv-full *
mmdet *
scikit-image *
scikit-learn *
torch ==1.13.
torchvision ==0.14.

.github/workflows/update-schema.yml actions

https://github.com/biigle/maia

Science Score: 39.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

BIIGLE MAIA Module

Installation

Configuration

References

Developing

Contributions and bug reports

Owner

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

packagist.org: biigle/maia

Rankings

Maintainers (1)

Funding

Dependencies