What is imaged ?

When polarized light passes through a diattenuating material, its intensity is reduced at a rate that is dependent on the incoming polarization. In linearly diattenuating materials, linearly polarized light is split into two components, one polarized parallel to the material axis with highest transmittance and one with polarization parallel to the lowest transmittance axis. Both axes are necessarily orthogonal to each other and correlate with the axis of molecular alignment. The differential transmittance, or diattenuation, is the difference between the maximum and minimum transmittance. The Diattenaution OpenPolScope measures and presents images of the transmittance, diattenuation, and the orientation of maximum transmittance in the specimen.

From Wikipedia: Diattenuation is related to dichroism, which has two related but distinct meanings in optics. A dichroic material is either one which causes visible light to be split up into distinct beams of different wavelengths (colours) (not to be confused with dispersion), or one in which light rays having different polarizations are absorbed by different amounts. The latter meaning describes a similar material property as diattenuation. Dichroism describes the property in terms of the material's absorption and diattenuation in terms of its transmittance.

Diattenuation setup
Diattenuation Setup (Inverted Scope)


The OpenPolScope augments the traditional polarizing microscope with specific hardware and software components.

Required hardware components:

General: Wide-field microscope stand with monochromatic light source, such as a halogen lamp with bandpass filter, for best results use strain-free objective and condenser optics;
CCD or equivalent camera supported by Micro-Manager software;
Computer with Windows 7, ImageJ, and Micro-Manager installed.

Diattenuation OpenPolScope specific: LC universal compensator, or filter wheel with linear and/or circular polarizers.

The LC universal compensator is made of a linear polarizer and two variable retarder plates implemented as liquid crystal devices. Unpolarized light enters on the side of the linear polarizer and exits as polarized light whose polarization can be set to any state, including circular polarization and linear polarization of any orientation. The LC settings are computer controlled through an electronic controller box.

The liquid crystal devices for the universal compensator can be custom ordered from several manufacturers.

Alternatively, a filter wheel loaded with polarizers rotated to the required orientations can be used instead of the LC universal compensator.

The OpenPolScope Group at the MBL can assist in acquiring and optimizing the installation of hardware and software components. See Services.

OpenPolScope Software

The OpenPolScope software synchronizes the LC or filter wheel settings and image acquisitions, calculates the transmittance, diattenuation, and polarization orientation for each resolved image point, and presents the results as images.

Diattenuation is one of three imaging modes of the OpenPolScope software which is built as Micro-Manager and ImageJ plugins.

Pol-Acquisition is a Micro-Manager plugin and is used for acquiring images. 

Pol-Analyzer is an ImageJ plugin and is used for viewing and reprocessing data. The Pol-Analyzer plugin requires Micro-Manager to be installed for reading image data previously acquired using Pol-Acquisition.

The transmittance is typically measured as the fraction of light transmitted through the attenuating specimen. Differential transmittance is measured either as the diattenuation or the ratio of maximum to minimum transmittance, or simply the difference between maximum and minimum transmitted light intensity. The orientation of maximum transmittance is given as an angle to the horizontal reference axis in the image. The OpenPolScope software calculates all three quantities for every resolved specimen point and presents the results of the computations as images. Below, images of a Siemens star composed of 36 wedge pairs etched into a thin metal film illustrate the computed results.

In the transmittance image, dark image regions correspond to metal wedges with low transmittance. Near the center, the pattern remains unresolved by the microscope optics.

In the diattenuation image, dark areas correspond to sample regions that have no or little diattenuation. Bright areas correspond to sample regions that are strongly diattenuating. In diattenuating regions, the polarized light gets split into two, mutually orthogonal components that are attenuated at different rates.

In the orientation image, each pixel value gives the orientation of the high transmittance axis as an angle between 0° and 180° with respect to the horizontal axis in the image.

Mean transmittance hi res
Anisotropy hi res
Orientation hi res


Siemens star Dichroism hi resMetal Siemens star imaged in diattenuation:  Differential transmittance of Siemens star in metal MBL/NNF target. Logarithmically enhanced LUT. The hue gives the orientation of the high transmittance axis, which is radially aligned, except near the center where it has azimuthal alignment.





Clofazimine - Gus Rosania, Department of Pharmaceutical Sciences, University of Michigan College of PharmacyClofazimine: Diattenuation image of clofazimine inclusions in spleen cryosection of a treated mouse, measured at 546 nm (in green) is overlayed on measurement at 630 nm (in red).  This indicates chromatic dispersion of the diattenuation of these crystals.

(From an on-going research collaboration with Gus Rosania, Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy)





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Last Page Update on July 24 2015 17:49