Features¶
pycromanager
has several options for interacting with micro-manager which can be used independently or in combination. The high level APIs described in Acquisitions are usually the best place to start. They describe how to run standard multi-dimensional acquisitions (i.e. Z-stacks, multiple XY posisitons, etc.), customized ones with abitrary axes and hardware settings, or ones generated through the Micro-magellan GUI using the pycromanager Acquisition
class. Acquisition
’s support customization such as modifying image data on-the-fly, controlling acquisition in response to data, integrating non-micro-manger supported hardware, running high-speed acquisitions with hardware TTL triggering, and using customized visualization/data saving. The data acquired by Acquisition
’s can be read into numpy
or dask
arrays using the Dataset
, as described in Reading acquired data.
For less complicated experiments (e.g. just snapping images on a camera, moving a single piece of hardware), Controlling Micro-Manager core might be a good place to start.
Finally, for experiments that require Java-based micro-manager plugins or already work well with existing beanshell scripts, try Micro-manager Java APIs or Calling custom Java code.