pygellan 0.0.5

Open source microscope control using python

Pygellan

Pygellan is a Python library for enabling microscope acquisition control and data analysis. It works together with the Micro-manager plugin, Micro-magellan. Currently, the two main features of pygellan are hardware control/data acquisition and data reading.

Setup

1. Install pygellan using pip install pygellan (Pygellan is tested with Python 3.6 but should also work with other versions of Python3)

2. (If using pygellan for acquisition control), download and install Nico Stuurman's 2.0gamma build of micro-manager. Latest nightly builds can be found here

Acquisition control

Note: acquisition control APIs are still actively being developed. Feedback and suggestions are welcome on the issues tab of this repository.

To use Pygellan for acqusition control, simply open the micro-manager2.0gamma GUI as usual and launch the Micro-magellan plugin. Start a python process in a way of your choosing (e.g. terminal, IDE, Jupyter notebook). Type:

from pygellan.acquire import MagellanBridge

bridge = MagellanBridge() #establish communication with Magellan

If the bridge object is created successfully, you are connected to Micro-Magellan and can use the rest of the pygellan.acquire API.

Controlling the Micro-manager core

The micro-manager core provides low-level functionality like capturing images and controlling individual devices. An example can be seen here.

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 Pygellan ultimately calls) can be found here.

Controlling Micro-magellan acquisitions

(Under active development)

See this example for how to start and stop Micro-magellan acquisitions through Python.

Reading data in Python

(Example coming soon...)