Image Data Transfer to R with ImageJ and Bio7 2.0

December 9, 2014

(This article was first published on » R, and kindly contributed to R-bloggers)


In the new version of Bio7 2.0 i added some new easy to use functions to transfer image data from ImageJ to R. For example, you can now drag a folder of images on the ImageJ-Canvas
view, open them memory efficient as a virtual stack in ImageJ and transfer them with one action as a list (or raster stack) to R.

With the new or improved actions it is possible to:

  • Transfer an ImageJ stack or virtual stack to R (RGB data or selected datatype will be transferred as a list).
  • Optionally transfer the stack as a raster stack (if the “raster” package is installed).
  • Transfer measured “Particles”  values from the “Results Table” from ImageJ to R.
  • Transfer values from an opened ImageJ “Results Table”.


Beside this new or improved actions there are many other methods available to transfer image data, selected pixel or selected coordinate data from ImageJ to R.

For an overview of the different functions i created a video playlist on YouTube how Bio7 can effectively asssist in the transfer and statistical analysis of image data (with the help of ImageJ and R).


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