Living Image 3.1

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B. Preferences B.6 3D Analysis 188 Table B5 Tissue properties preferences Item Description Index of Refraction The software automatically sets the internal medium index of refraction based on the selection in the Tissue Properties list Plot Tissue Properties Choose this option to display a graph of the absorption coefficient (μa), effective attenuation coefficient (μeff), and reduced scattering coefficient (μ’ s or μsp). Source Spectrum Choose this option to display the source spectrum. Apply to DLIT/FLIT Choose this option if the settings are for the Properties tab in the FLIT or DLIT tools. Planar Spectral Imaging Choose this option if the settings are for Properties tab in the Planar Spectral Imaging tools. Figure B.8 Set 3D analysis preferences (left) for the DLIT reconstruction tools (right) Table B6 3D analysis preferences Item Description System Select the IVIS Imaging System from the drop-down list. Angle Limit (deg) The angle between the object surface normal and the optical axis. For more details, see page 239. Kappa Limits Kappa (κ) is a parameter that is searched during a reconstruction to determine the best fit to the image data. Small values of kappa tend to favor deeper sources, while large values favor more shallow sources. For more details, see page 240.
<strong>Living</strong> <strong>Image</strong> ® Software User’s Manual Table B6 3D analysis preferences Item Description N Surface Limits The maximum number of surface intensity points to use in the reconstruction at a given wavelength. The range is 200 to 800 and the default is 200. The time required for reconstruction is shortest for smaller values of N (for example, 200). However, a large N value may give a more accurate result because more data are included in the fit. Voxel Size Limits Voxels are the small cubes of space inside a subject, each of which contains a light source (much like a pixel in a 2D image). The DLIT reconstruction begins with large voxels, specified by the voxel size limit (the length of a side of the voxel cube in mm). At each iteration, the algorithm reduces the size of the voxel by a factor of two until the optimum solution is found. The voxel size limits are a minimum of five and a maximum of 10. The default range is set to 6-9 mm. A larger range of voxel limits ensures a more reliable solution, but requires more computational time. The default range of 6-9 is usually adequate to determine the optimum solution. Voxel Size Increment Uniform Surface Sampling NNLS + Simplex Optimization This is the step increment in voxel size, stepping from the minimum voxel size limit to the maximum voxel size limit. For example, if the voxel size limit ranges from 6-9 mm, a voxel size increment = 1 gives four starting voxel sizes (6, 7, 8, and 9 mm). The default increment of 1 mm is usually adequate, however smaller increments can be used if you want to sample finer voxel sizes. Smaller increments will significantly increase the time required for reconstruction. If this option is chosen, the surface data for each wavelength will be sampled spatially uniformly on the signal area. If this option is not chosen, the maximum ‘N surface elements’ will be sampled for the data. This means that the N brightest surface elements will be used as data in the reconstruction. Typically, non-uniform sampling is recommended if there is a single bright source, while uniform sampling is preferred if there are several scattered sources. If this option is not chosen, the software uses a linear programming algorithm to seek the solution (Simplex solution). If this option is chosen, the software also applies a non-negative least squares optimization algorithm at each iteration to provide a better solution for source power. The Simplex solution is more robust, but tends to underestimate the source flux in each voxel. Therefore, the NNLS + Simplex option is recommended. NNLS Weighted Fit Choose this option to weight the wavelength data proportionally to its intensity in the NNLS reconstruction. This option is especially useful if the intensity of longer wavelength data is orders of magnitude greater than the intensity of shorter wavelength data. 189
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Living Image 3.1

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