Easy 3D Stack Concatenater

Concatenate 3D stacks with registration using user-provided landmark points


A very simple manual registration tool. Concatenate a 3D stack to another 3D stack, by aligning them according to the positions of landmark points provided by the user. Two different scripts are available for this processing. One is to provide the landmark points by a text file, and another is to provide landmark points by Point ROIs.

A bit more detail: Fiji comes with a manual registration function called “Name Landmarks and Register” for registration of a 3D stack of a channel to another channel. In this case, the Z position of slices are supposed to be more or less similar in two stacks. The script presented here is for concatenating stacks in Z direction (the goal would be to concatenate a stack taken at the lower half to the upper half) using landmarks.

Input: Two 3D image stacks to be concatenated. In addition, one of the following input sources for landmark position is required.

  1. Two text files (.points files), each with several landmark points. There should be at least three landmarks.
  2. or Point ROIs selected in both stacks specify the landmark points.

Output: A concatenated 3D stack, newly created.


  • ImageJ (Only Point ROI input works)

  • Fiji (both scripts works)


Two different type of scripts are available depending on how you feed the landmark information to the script.

If you have landmark points in a text file, download easy3Dconcatenation.ijm and run the script.

If you want to provide landmark points by Point ROIs, download easy3DconcatenationROIs.ijm and run the script.

In both cases, instruction on how to run the ImageJ macro is available at here.


Preparation of landmark point files ( .point files )

To create landmark file, use [Plugins > Landmarks > Name Landmarks and Register]. There is a detailed description of the usage of this tool in ImageJ.net site. You will then have one file each for two stacks with “.point” extension added to the name of each stack file. These files should be present in the same folder where stack files are stored.

Setting Point ROIs

If you want to directly set PointROIs, use Point ROI tool. To make multiple points, press down SHIFT to add more points. To delete a point ROI, press down ALT and click that point ROI. At least three point ROIs must be set for each stack.


Run the corresponding script. Two stacks will be concatenated and aligned vertically along z-axis.