Acquisitions for XY Tiling Multiple Fields-of-View

Pycro-Manager supports specialized Acquisition types for specific applications. The current special types are all for imaging large samples by capturing multiple fields of view and stitching them together. These include:

XYTiledAcquisition - Images large samples by capturing multiple fields of view - Stitches images into a single contiguous image - Uses a multi-resolution file format for efficient visualization at multiple scales
ExploreAcquisition - Extends XYTiledAcquisition - Provides a user interface for XY and Z stage navigation - Allows interactive selection of imaging locations
MagellanAcquisition - Controls the Micro-Magellan plugin - Offers sample mapping, region of interest definition, and specialized 3D dataset collection

Stitching acquired images

For these acquisitions the images are acquired in a grid pattern and then stitched together. The stitching can be done automatically by setting the stitched argument to True in the as_array method. This will return a Dask array that is a single contiguous image, and doesn’t pull individual tiles into memory until they are needed. This is useful for large images that don’t fit in memory.

dask_array = dataset.as_array(stitched=True)

XYTiled Acquisition

XYTiled Acquisitions support imaging of large samples by tiling multiple images together. Data is saved in a multi-resolution pyramid for efficient viewing at different zoom levels.

Note

This functionality requires a correctly calibrated affine transform matrix in the current configuration. Calibrate using the pixel size calibrator in Micro-Manager (Devices–Pixel Size Calibration).

Different XY fields of view can be acquired adding row and column indices in the axes of the acquisition event.

Usage:

from pycromanager import XYTiledAcquisition

with XYTiledAcquisition(directory='/path/to/saving/dir', name='saving_name', tile_overlap=10) as acq:
    # 10 pixel overlap between adjacent tiles

    # Acquire a 2 x 1 grid
    acq.acquire({'axes': {'row': 0, 'col': 0}})
    acq.acquire({'axes': {'row': 1, 'col': 0}})

Explore Acquisitions

Explore Acquisitions extend XYTiled Acquisitions with a graphical interface for user-controlled image acquisition:

Micro-Magellan Acquisition

Another alternative is to launch Micro-magellan acquisitions. These include both regular and explore acquisitions.

Micro-Magellan acquisitions can be run using the MagellanAcquisition class. The class requires as an argument either magellan_acq_index or magellan_explore. The former corresponds to the position of the acquisition to be launched in the Acquisition(s) section of the Micro-Magellan GUI. Passing in 0 corresponds to the default acquisition. Greater numbers can be used to programatically control multiple acquisitions. The latter corresponds to explore acquisitions, which can be launched by setting the magellan_explore argument equal to True.

from pycromanager import MagellanAcquisition

# no need to use the normal "with" syntax because these acquisition are cleaned up automatically
acq = MagellanAcquisition(magellan_acq_index=0)

# Or do this to launch an explore acquisition
acq = MagellanAcquisition(magellan_explore=True)

# Optional: block here until the acquisition is finished
acq.await_completion()

Like the other mechanisms for running acquisitions, Micro-Magellan acquisitions can be used with Acquisition hooks and Image processors.