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OpenPolScope Installer

The OpenPolScope Installer will install OpenPolScope software which is built as a Micro-Manager and ImageJ plugin. The Pol-Acquisition plugin is a Micro-Manager plugin required for acquiring data. The Pol-Analyzer plugin is used to open, view and re-process the OpenPolScope datasets (few examples included).

Requirements: Micro-Manager, Fiji or ImageJ needs to be installed. Recommended version Micro-Manager 1.4.22
Current Version: 3.20b (10-12-2018) ChangeLog

To learn about the users interested in OpenPolScope and their research areas, we ask you to register before downloading the installer.

Register   >>     Download Windows    ||    Download Mac   >>     Installation wizard    >>     Pol-Acquisition     ||     Pol-Analyzer

Note: If you experience an update error with ImageJ please download ij.jar from this location and replace your existing ij.jar located in the installation folder.

Conditions of use
  • You are free to use this software for research purposes, but you should not redistribute it without our consent.
  • In addition, we expect you to include adequate citations and acknowledgments whenever you present or publish results that are based on it.

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.

OpenPolScope Demo 1

 

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.

OpenPolScope Demo 2

 

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

OpenPolScope Demo 2

 

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.

OpenPolScope Demo 3

 

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

OpenPolScope Demo 4

 

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

OpenPolScope Demo 5

 

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

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

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)

OpenPolScope Demo 1

 

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.

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

Finish the wizard by saving the file

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

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.

OpenPolScope Demo 1

 

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.

OpenPolScope Demo 1

 

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

OpenPolScope Demo 1

 

OpenPolScope Pol-Analyzer

Starting Pol-Analyzer

OpenPolScope Demo 6

 

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

OpenPolScope Demo 7

 

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

OpenPolScope Demo 9

 

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

OpenPolScope Demo 10

 

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

OpenPolScope Demo 8

 

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

OpenPolScope Demo 11

 

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

OpenPolScope Demo 12

 

Load an existing dataset.

OpenPolScope Demo 13

 

Create a dataset.

OpenPolScope Demo 131

 

Loaded view of a dataset.

OpenPolScope Demo 14

 

Synthetic dataset.

OpenPolScope Demo 141

 

 

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Last Page Update on November 16 2018 15:02