OpenPolScope software implements instrument control, image acquisition and processing algorithms for rapidly imaging optical anisotropies in three different modes: birefringence, polarized fluorescence, and diattenuation.  Our software leverages popular open source, Java-based tools for biological microscopy, including ImageJ, ImageJ2, Fiji, Micro-Manager, and OME.  (also see SciJava )  This means that the software is 'agnostic' with respect to both operating systems and hardware devices/instrumentation.  OpenPolScope software is implemented as plugs for Micro-Manager and ImageJFiji.


Instrument control and image acquisition are accomplished using software written in Java that we have developed for this purpose called Pol-Acquisition.  Several acquisition modes are available: Birefringence, Polarized Fluorescence, and Diattenuation.  This system acquires an ordered sequence of images with varying polarization states that are defined as different 'channels' in Micro-Manager.  As datasets are acquired, the processed results are displayed and saved.  (See Analyzer section below.)  The system also provides instrument calibration routines, data and metadata management, and acquisition of background datasets.  Since it is a plugin for Micro-Manager, Pol-Acquisition integrates into the multi-dimensional acquisition process provided by Micro-Manager, so time series, z-sections and multiple positions are all supported.


The Pol-Analyzer performs processing algorithms for generating pixel maps of optical anisotropies in the specimen.  One map depicts the magnitude of anisotropy, irrespective of the orientation of the specimen in the plane of view. A second map depicts the orientation of the anisotropy, such as the slow axis of birefringent objects.

The Pol-Analyzer software is used for viewing and re-processing images and data acquired with the Pol-Acquistion software in any of the imaging modes.  Pol-Analyzer  is an ImageJ plugin which utilizes Micro-Manager libraries.

Imaging Modes

The OpenPolScope plugins (Pol-Acquisition & Pol-Analyzer) use a Mode based architecture utilizing Micro-Manager's multi dimensional & multi device approach. A Mode can be simply defined as an optical property that can be computationally determined based on n images acquired at n optical states. The Mode sub-plugins which are specific to Pol-Acquisition and Pol-Analyzer defines the type of device required (VariLC, Meadowlark LC, generic filter wheel) and a computation algorithm that would produce the computed images.

Images acquired with the OpenPolScope software represent the magnitude of specimen (birefringence) or anisotropy (polarized fluorescence & diattenuation), independent of its axis orientation, and display the measured magnitude in shades of gray or pseudo-color. In addition to the magnitude or anisotropy, the OpenPolScope software also measures the orientation axis at each image point. Thus, OpenPolScope software images display measured optical parameters that can be directly interpreted in terms of molecular organization in the specimen.

Other Software

We design and develop some additional software:

Micro-Manager Plugins

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Last Page Update on December 04 2014 16:32