Installation

ZIP Release

To install Microscope Automation for use on a ZEN Microscope, follow these steps:

  1. Copy the ZIP from the latest release by clicking here and selecting microscope_automation.zip

  2. Extract the contents of microscope_automation.zip to the location of your choice.

  3. Run Export_ZEN_COM_Objects.bat from inside the extracted folder.

  1. You may have to run as an administrator for it to work properly.

  1. Start the microscope and run XY stage, focus, and any other necessary calibrations.

  2. Run microscope_automation.exe from inside the extracted folder.

  1. When prompted, select the workflow preference file you wish to use, first checking all settings are configured as you wish.

For non-ZEN systems, simply skip Step 3.

Pip Installation

To install Microscope Automation, run this command in your terminal:

$ pip install microscope_automation

This is the preferred method to install Microscope Automation, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

From Sources

The sources for Microscope Automation can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/aics-int/microscope_automation

Or download the tarball:

$ curl  -OL https://github.com/aics-int/microscope_automation/tarball/master

Once you have a copy of the source, you can install it with:

$ python setup.py install

Packaging the ZIP

Simply follow the instructions on Deploying in Allen Institute Contribution Agreement.

GitHub Actions is configured to package the ZIP and publish to PyPI whenever a new version is pushed to the stable branch.