Installing

Microscope is available on the Python Package Index (PyPI) and can be installed like any other Python package. The short version of it is use pip:

pip install microscope

Note that you need to have Python and pip already installed on your system.

Requirements

Microscope can run in any operating system with Python installed but individual devices and intended usage may add specific requirements:

  • hardware performance: control of devices at high speed, namely image acquisition at very high rates, may require a fast connection to the camera, high amount of memory, or a disk with fast write speeds. In such case, it may be advantageous to have a dedicated machine for the camera.
  • external libraries: control of many devices is performed via vendor provided external libraries which are often limited to specific operating systems. For example, Alpao does not provide a library for Linux systems so control of Alpao deformable mirrors is limited to Windows. See the Dependencies sections below.

If there are multiple devices with high resources or incompatible requirements they can be distributed over multiple computers. For example, two cameras acquiring images at a high frame rate or a camera that requires Windows paired with a deformable mirror that requires Linux. See the Examples section.

Dependencies

Microscope has very few dependencies. All are Python packages available on PyPI and will be automatically resolved if Microscope is installed with pip. However, the interface to many devices is done via an external library (or SDK, or driver) that is only provided by the device vendor.

To identify if an external library is required, check the associated module documentation. If an external library is required, contact the device vendor for install instructions. Cameras, deformable mirrors, and spatial light modulators all require an external library. Filter wheels, lasers, and stages typically do not but there are exceptions.

Development sources

Microscope development sources are available on github. To install the current development version of Microscope:

git clone https://github.com/MicronOxford/microscope.git pip
pip install --no-index microscope/

Also consider using editable mode if you plan to make changes to the project:

pip install --no-index --editable microscope/

Multiple Microscope versions

Python package system will not by default handle multiple versions of a package. If installing from development, beware to not overwrite a previous installation. A typical approach to address this issue is to use virtual environments.

Un-merged features

Many features are still in development and have not been merged in the master branch. To try such features, you will need to know the branch name and the repository where such feature is being developed. For example, to try Toshiki Kubo’s implementation of the Mirao52e deformable mirror:

git remote add toshiki https://github.com/toshikikubo/microscope.git
git fetch toshiki
git checkout toshiki/mirao52e
pip install --no-index ./