bellameta 1.2.0

Metadata service for digital pathology WSI scans

Ballatrix Metadata

A microservice managing metadata of whole slide image (WSI) scans for digital pathology applications.

It operates on a storage sqlite database created by the bellastore package.
This database is particularly helpful when querying metadata of 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/bellameta.

Binary installers are available at PyPi.

pip install bellameta

Usage

Under docs/.env you find a simple template for an .env file that needs to be located in your current environment and hold the path to a yaml config file. A minimal config file is provided under docs/bellameta.yaml. This config defines the valid Cohort and Task types accesible by the package:

from dotenv import load_dotenv
load_dotenv()

from bellameta.types import Cohort
print(Cohort.list())

In order to add metadata to a cohort of scans, a child class of the abstract base class Metadata needs to be implemented:

from pamly import Diagnosis, Stain

from bellameta.database import Db
from bellameta.types import Cohort, Task
from bellameta.base_metadata import Metadata

class Example(Metadata):
    '''
    An example class inheriting from Metadata.

    We imagine this class to implement the metadata of a new cohort of scans that just arrived from the clinic.
    '''

    def __init__(self, db: Db):
        # here we need to specify the absolute path to the ingress directory as given in the ingress table
        # this serves as the identifier for our cohort
        super().__init__(db, '/tmp/tmpytfd3_47/example_cohort')
    def get_cohort(self, hash):
        # typing for cohorts is provided via bellameta/types
        return Cohort.Example.to_string()
    def get_stain(self, hash):
        # typing for stains is provided via pamly
        return Stain.to_string(Stain('HE'))
    def get_task(self, hash):
        # typing for tasks is provided via bellameta/types
        return [Task.Subtyping.to_string()]

In order to write this metadata to the database the class needs to be instantiated:

example = Example(db=db)
example.write_many()

Documentation

Along with the source code, under docs/demo.ipynb, we provide a demo leading you through the features of this package via an application scenario.