apis.rst

API Reference

Installation

.. currentmodule:: mmpycorex

.. autofunction:: download_and_install_mm

.. autofunction:: find_existing_mm_install

Acquisition event specification

The following shows all possible fields in an acquisition event (not all of which are required). An acquisition event which does not contain either the 'channel' key or the 'axes' key will not acquire an image, and can be used to control hardware only.

event = {
      # A dictionary with the positions along various axes (e.g. time point index,
      # z-slice index, etc.).
      'axes': {
              # Axis names can be any string
              'axis1_name': 1,

              # They can take integer or string values
              'axis2_name': 'first_position',

              # "channel" is a special axis name which will lead to different positions being
              # overlayed in different colors in the image viewer
              'channel': 'DAPI',

              # If an XYTiledAcquisition is being used, "row" and "column" are special
              # values that the acquisition engine will convert into stage coordinates,
              # laying out the acquired images in a grid
              'row': 1,
              'column': 0,

              },

      # Config groups can be used to control groups of properties
      'config_group': ['name_of_config_group', 'name_of_preset'],

      'exposure': 10.6, # exposure time in ms

      # Z stages
      # The 'z' field controls the default z stage device (i.e. the Core-Focus device)
      'z': 123.45, # the z position in um

      # Alternatively the device can be specified by name, or multiple devices can
      # be controlled by providing their names and positions in um
      'stage_positions':
                      [['z_stage1_name': 12.34],
                      ['z_stage2_name': 1234.566]],


      # For timelapses: how long to wait before starting next time point in s
      'min_start_time': 100

      # For XY stages
      'x': 123.4, # positions in um
      'y': 567.8,



      # If using a camera other than the 'Core-camera', it can be specified by name here
      'camera': 'a_camera_device_name',


      # Other arbitrary hardware settings can be encoded in a list of strings with
      # each entry containing the name of the device, the name of the property,
      # and the value of the property
      'properties': [['DeviceName', 'PropertyName', 'PropertyValue'],
              ['OtherDeviceName', 'OtherPropertyName', 'OtherPropertyValue']],


      # Custom metadata can be added to the event, which will be added to the metadata
      # of the resultant image under the 'tags' key
      'tags': {
              'whatever_you_want_here': 54,
              'something_else': 'here'}


      }

Acquisition APIs

.. currentmodule:: pycromanager.acquisition.acquisition_superclass

.. autoclass:: Acquisition
        :members:

.. currentmodule:: pycromanager

.. autoclass:: AcqNotification
    :members:

multi_d_acquisition_events

.. autofunction:: multi_d_acquisition_events

Adaptive acquisition

.. autoclass:: AcquisitionFuture
    :members:

Specific acquisition types

.. autoclass:: XYTiledAcquisition
        :members:

.. autoclass:: ExploreAcquisition
        :members:

.. autoclass:: MagellanAcquisition
        :members:

Headless mode

.. autofunction:: start_headless

.. autofunction:: stop_headless

Dataset

.. currentmodule:: ndstorage

.. autoclass:: Dataset
        :members:

.. currentmodule:: ndstorage

.. autoclass:: NDTiffDataset
        :members:

.. autoclass:: NDTiffPyramidDataset
        :members:

Micro-Manager Core

The core API is discovered dynamically at runtime, though not every method is implemented. Typing core. and using autocomplete with IPython is the best way to discover which functions are available. Documentation on for the Java version of the core API (which pycromanager calls) can be found here.

.. currentmodule:: pycromanager

.. autoclass:: Core
        :members:

Java objects and classes

.. autoclass:: JavaObject
        :members:

.. autoclass:: JavaClass
        :members:

Convenience classes for special Java objects

.. autoclass:: Magellan
        :members:

.. autoclass:: Studio
        :members: