RIKEN Center for Biosystems Dynamics Research, Laboratory for Morphogenetic Signaling (Hayashi Lab.)


ImageJ Plugins

Registration plugin for HyperStack

Registration for the stack image along the time axis

** In ver.20200731 or later, Template Matching method using opencv, javacv, javacpp has been added. For this reason, this plugin needs to download the binary file from the following site and be installed in the plugin folder.

JavaCV : https://github.com/bytedeco/javacv

Please use this for Fiji which has JavaCV1.4 series installed.

Main function:

  • Registration by several methods
  • Manual alignment
  • Projection with range specification
  • Cross section view
  • Load and Export the file type of mq(.ixo) *coordinate only


Basic function sample: trachea, fusion cell registration

Update log:

~ update 20220317 ~

  • Fixed a bug that prevented right-clicking (context menu invocation) on tables on some computers.
  • Added a paste function by control+v or commad+v to work around this bug
  • Adding function for Row in the Table
  • control + 1 : Put the previous row values in the selected line
  • control + 2 : Put 0.0 in the selected line
  • control + 3 : Put the after row values in the selected line

~ update 20200803 ~

  • Fixed a bug that processing can only be done from the first frame

~ update 20200731 ~

  • Add a Template Matching method with opencv, javacv, javacpp
  • Therefore JavaCV is required in the plugin folder
  • It does not work well in Fiji because it has its own javacv related
  • Avoid the error that occurs when right-clicking when the selected row is cleared in table
  • Corrected manual operation when checking “Comparison is the current slice”
  • Fixed the behavior when checking “backward shift”

~ update 20190905 ~

  • Some fixes

~ update 20190724 ~

  • Fixed the problem that cross section image is not displayed in specific image

~ update 20190403 ~

  • Code correction due to behavior change of ImageJ 1.52n or later

~ update 20190107 ~

  • Fix the problems in combining numbers into tables due to sub-pixelation

~ update 20180913 ~

  • Fix the problem of cross section view due to sub-pixelation

~ update 20180613 ~

  • Improved to handle subpixel
  • *For this reason, it is necessary to be careful because the movement of the image when setting the sub-pixel uses the complement value

~ update 20170921 ~

  • Freeze phenomenon occurred when moving the T-axis quickly due to the previous update -> This problem was solved

~ update 20170920 ~

  • Solved the phenomenon that some operations become unstable in MacOS Sierra
  • *There is a possibility to instability on operating systems prior to Sierra.

~ update 20161209 ~

  • Change the file name from CoordinateShiftHyper to CoordinateShift.
  • Change the name of some UI

~ version up! 20160729 ~

  • Add range specification function in projection

~ update! 20160218 ~

  • Eliminate the problems with Make Orthogonal

~ version up! 20160202 ~

  • Refactoring
  • Supported only java1.8 because of optimization
  • Add shift method (phase only correlation method) * code only

~ update! 20150701 ~

  • Enhance collaboration with Orthogonal image
  • Stabilization of Orthogonal image(fix the problem that default LUT value appears for a moment)

~ update! 20150514 ~

  • Changed LUT settings to be “R”, “G”, “B” when using a 24-bit image (RGB image)

~ update! 20150507 ~

  • Fixed the problem that occurs when using single channel in OrthogonalImage.

~ version up! 20150501 ~

  • Added the function to export the original image and the combined image of Orthogonal Image
  • Added Export ixo function
  • *Supports only coordinate information

~ update 20150430 ~

  • Improvement of operation at the time of Orthogonal image display
  • *mprove stability and brightness adjustment problems

~ version up! 20150428 ~

  • Improvement the View Orthogonal Image
  • Display multiple channels
  • Supports composite image

~ version up! 20150416 ~

  • Add View Orthogonal Image function (display X-Z, Y-Z image)
  • When ROI is set, only that area is displayed.
  • Limited to display of selected channels only.
  • Calculation is not performed when not displayed.

~ version up! 20150304 ~

  • Add a Backward shift checkbox(*process from the end of the stack image)

~ version up! 20150303 ~

  • The waiting time was reduced by performing post-drag processing in the background.
  • Add abort function to interrupt processing

~ version up! 20150225 ~

  • Significantly reduce memory usage!
  • Reduce memory leaks and become more secure for continuous use by review of the design

~ version up! 20150113 ~

  • Add local registration function using ROI
  • Add checkbox to allow overwriting of shift amount

~ version up! 20150109 ~

  • Add the fast method
  • Rearrange the position of UI button