Circa is a graphical user interface (GUI) for use with homebuilt confocal imaging microscopes in the Wang lab. Our setups are based on National Instruments DACs and pulse counters, in combination with ThorLabs galvonometers and photon counting modules.

This program is built on PyDAQmx for instrument control, the wxPython widget toolkit, and matplotlib.

First, install wxPython. I've always had trouble installing this using pip, but have had success using conda, or the official wxPython binaries.

Next, install wanglib as directed on that Github page.

Finally, using pip:

$ pip install --user -e git+https://github.com/baldwint/circa.git#egg=circa

The --user flag is a good idea to prevent version conflicts with other users on the same machine. It's unnecessary if you have some other means of doing that (e.g., in a virtualenv).

Circa contains a several programs targeting a couple of different tasks.

The main confocal-imaging program is launched by typing

$ circa

If this doesn't work, try python -m circa or pythonw -m circa. This program scans galvonometers using a 12-bit DAC (NI-USB-6008 or NI-USB-6009) and counts photons with a pair of counters on some other NI-DAQ device.

To monitor a graph of counts per second, use

$ python -m circa.monitor

This is useful for optimizing the counts when doing fine focusing.

During coarse focusing and alignment, it is sometimes useful to have a quickly-refreshing image. This isn't possible with our usual DACs since there is no timing support, but we can get very fast scanning by pre-loading the scan pattern on a pair of Tektronix AFGs. To do this, use an alternate version of the confocal imaging program:

$ python -m circa.fast

Both of the imaging programs save data in a raw .npz format. These can be loaded back into the imaging program to re-use the scan settings, or into a separate viewer program just to see the image:

$ python -m circa.viewer

Parameters for the data aquisition - that is, the DAQ channels, GPIB addresses, and so on - can be configured in a file called circa.cfg in your home directory. An example configuration (for Andrew's cryogenic setup) can be found in circa_example.cfg.