... respectively.2.1
Often a problem in MATLAB, when often image matrices need to be transposed before display! 
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... system3.1
The one exception is that the .NET framework needs to be separately installed on older versions of Windows (2000 and earlier). 
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... distribution3.2
Which despite the name is required! 
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...(*.mat).10.1
This last type, *.mat, is the same format as *.matr, but with a different suffix. This has been phased out due to the obvious potential confusion with MATLAB .mat files, which are not used by BioImage Suite. 
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... map''.11.1
For those of you who remember your multivariate calculus: In multivariable integration we often have problems which are better solved by changing the variables. The classic case is mapping a problem from Cartesian $(x,y)$ to polar $(r,\theta)$ coordinates. In those integrations at the end of the conversion there is a scale factor $\vert J\vert$ (=$r$ in this case) which is the determinant of the Jacobian matrix between the two pairs of variables that quantifies the area (volume) ratio between the original small element $(\delta x,\delta y)$ and the mapped small element $(\delta r,\delta \theta)$. This is the same identical term, where in this case the two small elements are the original image voxels and the transformed image voxels. 
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