Open source microscope control using python
Project description
pycromanager
is a Python library for enabling microscope acquisition control and data analysis. It works together with Micro-manager and Micro-magellan.
Check out to the documentation for an idea of the capabilities and how to get started.
Have a cool example of something you've done with pycromanager
or an idea for improvement? Reach out on the issues page. Contributions/ideas/examples welcome!
Installing pycro-manager
- Download the lastest version of micro-manager 2.0
- Install pycro-manager using
pip install pycromanager
- Run Micro-Manager, select tools-options, and check the box that says Run server on port 4827 (you only need to do this once)
To verify everything is working, run the following code:
from pycromanager import Bridge
bridge = Bridge()
bridge.get_core()
which will give an output like:
Out[1]: JavaObjectShadow for : mmcorej.CMMCore
Troubleshooting
Upon creating the Bridge, you may see an error with something like:
UserWarning: Version mistmatch between Java ZMQ server and Python client.
Java ZMQ server version: 2.4.0
Python client expected version: 2.5.0
In this case case your Micro-manager version Pycro-manager versions are out of sync. The best fix is to download the latest versions of both. Uprgade to the latest Pycro-manager with:
pip install pycromanager --upgrade
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