Bio7 3.1 Released

I released a new version of Bio7. This update comes with a plethora of new features, improvements and bugfixes.


(Bio7 R ImageJ Analysis perspective - MacOSX, Dark Mode)

For those who don’t know Bio7. The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis and integrates ImageJ as an Eclipse plugin. The development started in 2004 with the first release in July 2007.

ImageJ Specific Release notes:

  • Bio7 3.1 RCP (Rich Client Platform) built upon Eclipse 4.14
  • Bundled with AdoptOpenJDK 13.0.2
  • Dynamic compilation now supports Java 13 by default
  • Updated ImageJ to version 1.52t(.51)
  • Added a new ImageJ macro debugger interface
  • Enabled Java code completion for the ImageJ API in the JDT Java editor
  • Added a new thumbnail action to the context menu of the ‘Navigator’ view to open image and LUT files of a selected directory (see animated *.gif below)

  • Changed the ‘Image-Methods’ view to show only R/ImageJ related actions (bidirectional transfer of image data, selection data, particle and cluster methods, etc.)
  • Added the ‘Geometry Selections’ view to the ‘R ImageJ Analysis’ perspective to transfer ROI selection coordinates as a list or georeferenced data geometries (using package ‘sp’ and Java GDAL)
  • Added the KMeans cluster algorithm to the ‘Cluster Pic’ action in the ‘Image-Methods’ view
  • Added a ‘Detach All Images’ action to transfer all opened tab images to a view (which can be moved and arranged like a separate window)
  • Improved the dark theme for all AWT components (especially on MacOSX and Linux)
  • Added new default macro editor templates
  • Improved the ImageJ plot windows
  • Improved the detached image view layout
  • Improved the canvas layout for HighDPI displays on Windows
  • The ‘R ImageJ Analysis’ perspective is now visible by default
  • Improved the ‘Pixel RM’ and ‘Pixel RM Stack’ action to transfer all ROI selections more efficiently, especially for VirtualStacks of ImageJ
  • Added a new option in the ‘Pixel RM’ and ‘Pixel RM Stack’ action to transfer ROI Manager selections signature names according to a separator char (handy for supervised classification with ImageJ and R)
  • Added a new stack transfer API method (‘imageFeatureStackToR’) to transfer whole stacks in a column layout (for pixel classification).

For the new classification ImageJ/R API and transfer methods I created a Java example here:

The complete release notes and installation instructions can be found here:

https://bio7.org/bio7-3-1-released/

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