Stackreg Plugin Download
Karolien Prisco
Those four types of transformation are available from the scroll list that should appear when the StackReg plugin is launched. The fifth transformation type (bilinear transformation), available in TurboReg, does not appear in StackReg because a combination of bilinear transformations does not generally result in a bilinear transformation. It is therefore not possible to propagate such transformations from slice to slice.
The dialog box of Figure 2 will appear upon launching StackReg, provided at least one image or stack is available, and provided the type of the current image is admissible. An explicit error message should appear otherwise. Clicking the [Cancel] button aborts the plugin. Setting a tickmark on the [Credits] checkbox and clicking the [OK] results in the information panel of Figure 3. Simply clicking the [OK] button applies the plugin to the current image or stack. The applied transformation is that which is selected in the [Transformation] scroll list.
The present plugin (StackReg) is used as a front-end to another plugin named TurboReg. Several mechanisms are at work to exchange data between these plugins. One of them involves temporary files which are written into the temporary directory that ImageJ defines. The location of this directory can be examined by issuing the macro command 'print(getDirectory("temp"));'. The names of the written files are
Opened your stack in Fiji.
Scroll through the stack until slice #10. Deleted it by Image > Stacks > Delete Slice
Ran the plugin Plugins > Registration > StackReg
Took about 30 seconds for the plugin to finish.
Not sure what the problem is, but if the zip contained *.java and *.class files, try deleting (or moving out) the *.java files.
I think Fiji tries to compile whenever it finds those. You only need the *.class files in the plugins folder.
I use a macro to run stackreg on all stacks in a directory. What I need is to run multistackreg on that directory and make it save the transformation matrices for each stack. Then I need to be able to do the same on another directory with the same number of stacks, but instead of having multistackreg actually registering the stacks, I want it to just load the transformation matrices from the first run, and apply them to the corresponding track in this directory.
pyStackReg is used to align (register) one or more images to a common reference image, as is required usually in time-resolved fluorescence or wide-field microscopy. It is directly ported from the source code of the ImageJ plugin TurboReg and provides additionally the functionality of the ImageJ plugin StackReg, both of which were written by Philippe Thevenaz/EPFL (available at ).
To install Turboreg I downloaded the Unix distibution (for my Ubuntu machine) and copied the extracted folder Turboreg to the ImageJ/plugins folder. Then opened ImageJ, opened an image, used image/Type/RGB stack to convert 2 images of same size to stack image and went to plugins/TurboReg/TurboReg and clicked on the menu and every time I do that with various images I get the following exception in the
StackReg/TurboReg are popular plugins for the alignment of series of images required in time-dependent microscopy to correct for sample drift and in multicolor super resolution microscopy to align the different color channels. These plugins are written in Java for the image processing software Fiji/ImageJ, one of the most widely used open source image analysis tools in life sciences.
To expand access to these tools, this project will port the pyStackReg package, a standalone Python package of the StackReg/TurboReg plugins, to napari as a proper plugin. This will provide the excellent functionality of the original StackReg/TurboReg plugins to the napari community.
I am using ImageJ to register or align a series of X-ray Computed Tomography Images. There is an ImageJ plugin called StackReg that does a pretty great job with several different algorithm choices to align the circular images for the cylindrical part we are doing CT on.
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