Architecture

Frontend

• language: TypeScript

• environment: Node.js (v20)

• framework: React (v18)

• middleware: Redux, Redux Toolkit, React Router

Directory Structure

Following is the summary of directory structure.

• frontend

  • src

    • api: handle API requests.

    • components: React components.

    • const: constants.

    • pages: Components set as element in Route component of react-router.

    • store: Redux store.

      • slice

        • Some

          • SomeActions.ts: create actions like async thunk from api response.

          • SomeSelectors.ts: select state from store.

          • SomeSlice.ts: define reducers.

          • SomeType.ts: define data type.

          • SomeUtils.ts: define utility functions if needed.

    • style: extra css files.

    • utils: common utility functions.

  • .env: Application environment variable definition file

    • Depending on usage, the following .env files are available

      • .env: Loads for all environments

      • .env.development: Used during development (yarn start)

      • .env.production: Used during production builds (yarn build)

    • Learn more

• api, components, store/slice directories are separated by its domain.

Backend

• language: Python (v3.8)

• framework: FastAPI

• handle workflow by snakemake.

Directory Structure

Following is the summary of directory structure.

• studio

  • alembic: files for database migration. database is used in multi-user mode.

  • app

    • Snakefile: File read by snakemake. It defines how to run workflow by language like Python.

    • common: common modules(not for specific domain)

      • core: define core functions.

      • dataclass: define dataclasses that are passed between nodes or used as visualize outputs.

      • db: database general configuration.

      • models: database models.

      • routers: define fastapi routers.

      • schemas: define pydantic schemas for api requests and responses.

      • wrappers: functions for algorithm nodes.

    • optinist: modules specific to calcium imaging data processing domain. It has same structure as common.

  • config: configuration files.

    • .env: Application environment variable definition file

    • logging:

      • logging.yaml: logging config for standalone mode. In standalone mode, logs are sent to streams.

      • logging.multiuser.yaml: logging config for multi-user mode. In multi-user mode, logs are sent to file (in logs dir). log file rotation settings are included.

      • you can manage log configurations by editing these files.

    • auth: put Firebase authentication secret files.

    • docker: backend Dockerfiles for each environment.

  • test_data: test data for unit tests.

  • tests: unit tests.

  • __main__.py: entry point of backend in production.

  • __main_unit__.py: core main unit. called by studio/__main__.py and main.py.

• main.py: entry point of backend in development.

• run_cluster.py: entry point for CLI run.