TransformJ Update

Posted by Erik Meijering on Aug 22, 2015; 9:51am
URL: http://imagej.273.s1.nabble.com/TransformJ-Update-tp5014108.html

Dear TransformJ users,

TransformJ 4.0.0 is now available (http://www.imagescience.org/meijering/software/transformj/) for ImageJ users and will soon also appear in the Fiji distribution.

It is a long-awaited major update. So long, in fact, that in the meantime many of you probably got used to the shortcomings of the package and found ways to work around them. Needless to say these work-arounds will no longer work with the new version, so you may need to update your code/macros a bit.

Apart from some cosmetic changes the most important fundamental change is that the Affine and Rotate plugins are now able to properly work with image stacks having anisotropic voxels. This means you no longer need to first resample your data to isotropic voxels (if this was part of your pipeline you will need to remove that step). The plugins offer the possibility to either sample the transformed image on the same grid (same anisotropy) as the input image (this is the default mode) or to resample the stack isotropically while transforming (an option to be selected by the user).

Even though this means TransformJ now finally works the way it should have from the beginning, perhaps some of you would like to keep the old behavior of the plugins. This is possible. The only thing you need to do then is temporarily set the voxel width/height/depth to 1.0 (which is what TransformJ has been assuming all along previously), then perform the transformation, and afterwards put these properties back to their old values.

For consistency with the Affine plugin (the most generic plugin of the package), two other changes were introduced. First, the Scale plugin by default no longer rescales the voxel properties in order to retain the physical image dimensions, but this is now an option (to be selected by the user). Second, the Translate plugin now assumes the translation distances to be in physical units (determined by the voxel properties), but an option has been added (to be selected by the user) to take these distances as voxel units.

Have fun transforming your data!

Erik

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