README

This is a BIIGLE module that offers the Magic SAM image annotation instrument.

Installation

1. Run composer require biigle/magic-sam.
2. Run php artisan vendor:publish --tag=public to refresh the public assets of the modules. Do this for every update of this module.
3. Configure a storage disk for the image embedding files. Set the MAGIC_SAM_EMBEDDING_STORAGE_DISK variable in the .env file to the name of the respective storage disk. The content of the storage disk should be publicly accessible. Example for local disks:

   'magic-sam' => [
       'driver' => 'local',
       'root' => storage_path('app/public/magic-sam'),
       'url' => env('APP_URL').'/storage/magic-sam',
       'visibility' => 'public',
   ],

   This requires the link storage -> ../storage/app/public in the public directory.

Configuration

Image embeddings are computed in jobs submitted to the default on the CPU. They require a queue worker Docker container that satisfies the Python requirements of this repository. Embeddings can be computed much faster on a GPU. You can cnfigure the queue name with the MAGIC_SAM_REQUEST_QUEUE and the device (cpu or cuda) with the MAGIC_SAM_DEVICE environment variables.

Image embedding files are automatically deleted after 30 days. You can configure this with the MAGIC_SAM_PRUNE_AGE_DAYS environment variable.

References

Reference publications that you should cite if you use Magic SAM 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

• Segment Anything Kirillov, A., Mintun, E., Ravi, N., Mao, H., Rolland, C., Gustafson, L., Xiao, T., Whitehead, S., Berg, A.C., Lo, W.Y. and Dollár, P., (2023). Segment anything. arXiv preprint arXiv:2304.02643. doi: 10.48550/arXiv.2304.02643

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.