clij - GPU-acceleration for ImageJ


clij is an ImageJ/Fiji plugin allowing you to run GPU-accelerated code from within Fijis script editor (e.g. macro and jython). CLIJ is based on ClearCLImglib2 and SciJava. It contains components for image filtering, thresholding, spatial transforms, projections, binary image processing and basic signal measurements.

FMRIB's Linear Image Registration Tool FLIRT


FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

FLIRT comes with a main GUI as well as three supporting guis:

  • ApplyXFM - for applying saved transformations and changing FOVs
  • InvertXFM - for inverting saved transformations
  • ConcatXFM - for concatenating saved transformations

3D affine transformation based on paired points


Using a text file containing 3D point coordinates as reference pairs, 3D image stack is transformed.

Track Processor Zero Origin

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Copy Pixel Size


This plugin copies the pixel size from the calibration of one image or stack to a second image or stack. This allows one to copy the spatial calibration from one stack to another.

A second dialog allows to enter the scale factors.

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KNIME Average Filter


Applies average filtering to images in n-dimensions