Installation wizard

The OpenPolScope software works with Micro-Manager, Fiji and ImageJ. However, for acquiring a dataset via Pol-Acquisition (Micro-Manager plugin) Micro-Manager is essential. The Pol-Analyzer (imageJ plugin) requires the basic Micro-Manager libraries in order to view and re-process datasets.

 

For this example we use Micro-Manager as our target. The default location is pre-populated if Micro-Manager is installed. If multiple copies of Micro-Manager are installed the last one is used. When installing in non Micro-Manager installations (Fiji or ImageJ) only demo device adapters are installed.

 

Setup will not proceed unless a valid Micro-Manager or ImageJ installation is specified.

 

Select the type of Install (default is Birefringence mode only). When installing in Fiji or other ImageJ installations a scaled down version of Micro-Manager is installed.

 

A User manual introducing Polarization is included which is a good start to familiarize with terms.

 

The OpenPolScope software is installed in the plugins folder. The Fiji and ImageJ variant also installs a copy of Micro-Manager.

 

OpenPolScope Pol-Acquisition

Start by initializing ImageJ. If this is a Micro-Manager installation Micro-Manager will start automatically otherwise go to ImageJ > Plugins > Micro-Manager

 

Start by defining a hardware configuration. Under 'Tools' in the Micro-Manager menu select Hardware Configuration Wizard

 

Add your Camera from the device list

For Abrio Systems: The camera used is a Lumenera Infinity series. Download and install Lumenera drivers INFINITY Camera Software v6.3.0 (23 MB)

 

If using a Universal Compensator as your Pol-Device select either VariLC or MeadowlarkLC from the device list. If using an Abrio system select VariLC as well and set baud rate to 115200 instead of the default 9600.

 

When using a MeadowlarkLC from the device list additional configuration will be required as follows.

 

If using a Filter Wheel as your Pol-Device select it from the device list and rename the device label 'PolWheel'.

 

 

Add your device delay (approximate time required for the device to change its state) settings. 100ms recommended for Liquid Crystal device.

 

Finish the wizard by saving the file

 

Start Pol-Acquisition located under the Plugins menu of Micro-Manager

 

A prompt will alert if OpenPolScope is installed for the first time

 

Select a root level directory with write permissions. A central location for all users is recommended though not a requirement.

 

If user specific root level directory is defined, then at startup Data Location will be need to be re-validated.

Important: Create a new User and then a new Session before using the software.

 

Once the above steps are completed Pol-Acquisition will start with the view below based on the last User and Session.
Note: In ver. 3.xx, the software will start with NoDevice tab and an appropriate mode needs to be selected via the Processing tab.

 

Additional Help documentation for Pol-Acquisition is available under the Help menu of Pol-Acquisition.

 

OpenPolScope Pol-Analyzer

Starting Pol-Analyzer

 

For Fiji/ImageJ: Pol-Analyzer will initialize Micro-Manager first since it is required for viewing and re-processing.

 

For Fiji/ImageJ: None should be selected when Micro-Manager initializes.

 

For Fiji/ImageJ: Since Pol-Analyzer requires data acquired using the Pol-Acquisition plugin select Cancel to use a Temporary directory.

 

Pol-Analyzer interface should now initialize with default values or from Pol-Acquisition settings.

 

For detailed description please refer to the Pol-Analyzer manual.

 

To get started you can either create or load an existing dataset.

 

Load an existing dataset.

 

Create a dataset.

 

Loaded view of a dataset.

 

Synthetic dataset.