Bellatrix Storage

Organizing whole slide image scans (one of the main data sources in digital pathology) by automatically creating a storage and keeping track of new data via an sqlite database. This database is particularly helpful when querying specific slides for downstream tasks via our custom digital pathology API bellapi.

Installation

The source code is currently hosted under https://github.com/spang-lab/bellastore.

Binary installers are available at PyPi.

pip install bellastore

Usage

Installing the package will automatically install the binaries for the two main scripts.

• bellastore-insert inserts new scans from ingress to storage
• bellastore-backup backups the sqlite database

# For dry run (scans will not be moved and database will not be changed)
bellastore-insert --root_dir <directory holding storage and backup> \ 
                        --ingress_dir <directory_holding_new_scans> \
                        --sqlite_name <name of sqlite database>

# Moving slides and recording in database
bellastore-insert --root_dir <directory holding storage> \ 
                        --ingress_dir <directory_holding_new_scans> \
                        --sqlite_name <name of sqlite database> \
                        --move

# Create backup of database in backup directory
bellastore-backup --root_dir <directory holding storage and backup> \
                            --sqlite_name <name of sqlite database>

Documentation

Along with the source code, under docs/demo.ipynb we provide a demo of the main usecase of the package, that leads you trough the steps of the main integration test tests/test_db_fs.py::test_classic.
The package comes with a test suite, serving to demonstrate the functionality of each unit of the package.