Plugin Installation

Install navigate

This guide assumes that the latest version of navigate has been installed and is functional. If not, please refer to the installation guide in navigate’s documentation.

Install navigate-mmcore-plugin

Once navigate is installed, the next step is to install the navigate-mmcore-plugin. Broadly, this consists of activating the navigate environment, cloning the navigate-mmcore-plugin repository, and installing the plugin.

Activate the navigate Environment

(base) MyComputer ~ $ conda activate navigate

Clone navigate-mmcore-plugin

Clone the latest version of navigate-mmcore-plugin, change your directory to its root folder (e.g., D://path/to/navigate-mmcore-plugin/, and install the libraries necessary to run navigate-mmcore-plugin using the following command:

(navigate) MyComputer ~ $ pip install -e .

Run navigate Software

(navigate) MyComputer ~ $ navigate

Note

If you are running the software on a computer that is not connected to any microscope hardware, you can add the flag -sh (--synthetic-hardware) to launch the program:

navigate -sh

Installing the navigate-mmcore-plugin

Once navigate is running, you can install the plugin by selecting the menu Plugins ‣ Install Plugin and selecting the navigate-mmcore-plugin folder. navigate will automatically install the plugin and prompt you to restart the software. After restarting, the plugin will be available in the navigate

Install Micro-Manager

Once navigate and the navigate-mmcore-plugin are installed, you need to install and configure Micro-Manager.

Download the nightly build of Version 2.0 of Micro-Manager from the Micro-Manager website

Detailed information on how to install Micro-Manager can be found here.

Configure Devices in Micro-Manager

Next you should configure the devices in Micro-Manager and save the configuration file. This is done by opening the Micro-Manager and using the Hardware Configuration Wizard. Importantly, all of the devices should be confirmed functional in Micro-Manager before proceeding to the next step.

Installation details for each device can be found here.

Configure your Windows Environment

Next, you need to make sure that Windows knows where to find the Micro-Manager device files. This is done by adding the path to the Micro-Manager device files to the Windows environment variables.

Open the Windows Control Panel.
Click on System and Security.
Click on System.
Click on Advanced system settings.
Click on Environment Variables.
Double click on the Path variable in the System variables section.
Click on New and add the path to the Micro-Manager device files. This is typically C:\\Program Files\\Micro-Manager-2.0.

Once this is complete, restart your Anaconda Prompt so that the new Path variable is recognized.

Modify the Configuration Files

Configure navigate-mmcore-plugin configuration file.

Next, you will need to modify the configuration file for the navigate-mmcore-plugin. Provide it with the name of the plugin, the view type (e.g., if it should be displayed as a tab or a popup), and the path to the Micro-Manager device adapter.

name: MMCore Plugin
view: Popup # Tab or Popup if has an GUI

device_adapter_path:
  - "C:\\Program Files\\Micro-Manager-2.0"

Configure the navigate configuration file.

Finally, you will need to modify the navigate configuration file to include the device that you wish to use. For example, if we were to be configuring MMCore to use a Physik Instrumente (PI) stage, the configuration file would look like this:

stage:
  hardware:
    -
      type: MMCore
      serial_number: 119060508
      config_path: "C:\\Program Files\\Micro-Manager-2.0\\test.cfg"
      axes: [z] # axes used in navigate
      axes_mapping: [z] # axes used in MMCore

    -
      type: PI
      controllername: E-709
      stages: P-726.1CD
      refmode: ATZ
      serial_number: 0116049747
    -
      type: SyntheticStage
      serial_number: 01234

Here, the first stage in the list, which is type MMCore, is the stage that will be used by the navigate-mmcore-plugin. The serial_number is the serial number of the stage and the config_path is the path to the Micro-Manager configuration file.

Launch the Software

Once the configuration files have been modified, you can launch navigate and the navigate-mmcore-plugin. The plugin will automatically connect to the Micro-Manager device adapter and the devices will be available for use in navigate.