acquisition.yaml

acquisition:
  metadata:
    driver: exaspim_control.metadata.aind_metadata_class
    module: AINDMetadataClass
    init:
      metadata_dictionary:
        instrument_type: exaSPIM
        subject_id: '123456'
        experimenter_full_name: [adam glaser]
        chamber_immersion:
          medium: other
          refractive_index: 1.33
        x_anatomical_direction: Anterior_to_posterior
        y_anatomical_direction: Inferior_to_superior
        z_anatomical_direction: Left_to_right
      date_format: Year/Month/Day/Hour/Minute/Second
      name_specs:
        deliminator: _
        format: [ instrument_type, subject_id ]
  operations:
    vp-151mx:
      # imaris:
      #   type: writer
      #   driver: voxel.writers.imaris
      #   module: ImarisWriter
      #   init:
      #     path: D:\\
      #   properties:
      #     compression: lz4shuffle
      #     data_type: uint16
      aqz:
        type: writer
        driver: voxel.writers.zarr
        module: ZarrWriter
        init:
          path: D:\\
        properties:
          compression: zstd
          data_type: uint16
          chunk_size_x_px: 128
          chunk_size_y_px: 128
          chunk_size_z_px: 32
          multiscale: True
          version: v3
      robocopy:
        type: file_transfer
        driver: voxel.file_transfers.robocopy_zarr
        module: RobocopyFileTransfer
        init:
          external_path: Z:\\scratch\\adam.glaser
          local_path: D:\\
        properties:
          verify_transfer: True
          max_retry: 3
          timeout_s: 60
      # max_projection:
      #   type: process
      #   driver: voxel.processes.max_projection.cpu.numpy
      #   module: CPUMaxProjection
      #   init:
      #     path: D:\\
      #   properties:
      #     data_type: uint16
      #     x_projection_count_px: 3548
      #     y_projection_count_px: 2660
      #     z_projection_count_px: 2048
      # background_collection:
      #   type: routine
      #   driver: exaspim_control.routines.background_collection
      #   module: BackgroundCollection
      #   init:
      #     path: D:\\
      #   properties:
      #     data_type: uint16
      #     frame_count_px: 20
  tiles: []