In reply to this post by Ethan Cohen Dear Ethan, Reading your post, it seems to me that that you have the same application issues I went through and for which I have spend quite some time. It is written as a plugin for ImageJ. Consists of the following two mandatory fields, in that order:. The landmarks are reset to their default position when changing the distortion type. Only one color plane of the RGB stack is taken into account for registration; the transformation applied to the two remaining color planes will be adjusted accordingly. You need to restart ImageJ, open the movie only have 1 movie open at a time that you would like to eliminate drift from, and then go to the plugins drop down menu in Image J, move to the Stack Reg line and click on the StackReg box that appears. 
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To magnify an image, select the magnification tool and click in the image. Items to put in Plugins folder: To know the exact domain where the mean-square criterion has been applied, the user must himself perform an "AND" operation between the mask if any of the target image on one hand, and the returned mask of the warped source image on the other hand: Also, it is possible to specify cropping zones in the source and target images, which is useful when there is a reduced overlap between images, a situation that often arises when stitching together a mosaic of images.
In the manual mode, this automatic refinement procedure is disengaged.
During the registration process, the slice being registered is displayed; after the registration process is completed, the display returns to the slice that was the current one at launch time. Although TurboReg is scriptable, it is not recordable.
The columns are labeled sourceXsourceYtargetXand targetYin stackrey order. The format of the file is rigid; it is nevertheless possible to edit its numerical fields if desired.
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Those four types of transformation are available from the scroll list that should appear when the StackReg plugin is launched. You can choose various transformations, but probably the default choice rigid body is best.
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The dialog box of Figure 2 will appear upon launching StackReg, plguin at least one image or stack is available, and provided the type of the current image is admissible.
The configuration must have been previously created by TurboReg. Requires three landmarks in each image; the first landmark gives the overall pugin and the two remaining ones determine the rotation angle. The output image that results from the registration process is returned as a stack.
StackReg x,y translation values
You'll be free to use this stackret for research purposes, but you must not transmit and distribute it without our consent. Please note that an RGB-stack is a stack of three color components; it should not be confounded with a stack of RGB-color images: When accuracy is favored instead, the output image benefits from high-quality interpolation cubic spline.
The batch mode is not available for RGB stacks. A technical Javadoc documentation is available. You can restore a configuration of landmarks from a text file by clicking the button [Load Synapse Classification - The culmination of my graduate thesis was the use of interactive machine learning to classify synapses in array tomographic volumes.
stackreg function not available
It is written as a plugin for ImageJ. You can save the current configuration of landmarks in a text file by clicking the button [Save Now The plugin stackrsg accommodate grayscale images and RBG stacks.
ImageJ Interest Group [mailto: When speed is favored, the output image suffers from low-quality interpolation nearest-neighbor. Download This distribution is dated July 7, Before left and after right having applied the alignment procedure to an eye fundus.
Macro StackReg is scriptable and recordable. OK, I tried a few more.
ImageJ - StackReg x,y translation values
When a stack of color images is provided, the registration proceeds on a grayscale version that is built as a weighted sum of the red, green, and blue components—even when the stack is pseudo-color. The quality is always set to 'Accurate'. Is there a way to get the x,y, translation values out in a table for the aligned images translation coordinates relative to the reference image? The extractions will generate two folders in the plugins pluign named stackReg and TurboReg.
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