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


ImageJ Plugins

Plugin for performing PIV on time series images

Plugin for performing PIV on time series images


The LineProjection method used in CoordinateShift is used to calculate the amount of movement in each region of interest

This seems to enable faster processing than the method using basic correlation and FFT.

However, the possibility of poor accuracy and detectability is also conceivable. -> greatly improved with ver. 20180613

Processing of only the rectangular ROI selection part is also possible.

The original image is duplicated, and the display by Arrow ROI is also possible for the blank image.

Correct using 3×3 Median filter.


Download Manual.txt (Japanese)

Sample movie:

ver.20180613: Example of use, original image(https://sites.google.com/site/qingzongtseng/piv)
Process with width 32, height 32, overlap 50, extend value 1 on the image after correction using CoordinateShift. After that, make QuickTime movie with Save Mov

Update log:

~update 20210903 ~

  • Add Color Method
  • Hue : The color is determined in HSB format by adopting the saturation corresponding to the ratio of the distance by each arrow divided by the maximum distance within that series. (S: fixed at 1.0, B: saturation*1.5)
  • Absolute : Colorize the image into 8 colors (8 equal parts) using the Max length limit as the maximum value. If this value is set to 16, it corresponds to the old color coding.
  • Relative : Divide the distance of each arrow by the maximum distance of the series, and color-code it into 8 colors (8 equal parts).For the Length ratio limit, enter a value that multiplies the maximum distance.
  • Added minimum and maximum values to Color Box.
  • The minimum value is 0, the maximum value is the lower part converted to the actual value using the scale information stored in the image, and the upper part is the pixel value. (to the second decimal place).

~ update 20200915 ~

  • Changed the value of Length in SaveTSV so that it does not reflect the Extend value.
  • Fixed the issue that the Radian value stored in “Angle” in SaveTSV was calculated from the monitor coordinates.

~ update 20200914 ~

  • Changed Extend Value to change only the length of the arrow
  • Added Length limit value. The color coding of the arrows was abstracted by finding the ratio with the maximum length in the series as the denominator and standardizing with this value.
  • Addition of a function to display the color-coded sample image.
  • Changed to be able to save in Coordinate, Length, Angle (radian) in SaveTSV. Coordinate is the same as before, but for Length and Anglen, each value is stored as double as Row: PositionID, Col: Time.
  • Note: The sign of the radian value may be reversed in SaveTSV (Angle).

~ update 20190403 ~

  • Correspond to the specification change of ImageJ 1.52n or later

~ version up 20180613 ~

  • Shift of sub-pixel is possible by improvement of LineProjection method.
  • This has improved the accuracy.

~ update 20150604 ~

  • Code arrangement.
  • In addition, speeding up is achieved by parallelizing some processes.

~ version up 20151217 ~

  • Added the function to export coordinate data to tsv.

~ First uplaod 20150528 ~