Category Archives: Uncategorized

R Editor and ImageJ Plugin Update


Two new plugin updates are available for Bio7.

R Editor update:

The R editor plugin has been updated for the new R 4.1 grammar (shorthand function notation, native pipe operators). The new grammar is also considered in the code completion of the editor and in the R-Shell (e.g., function calls, pipes with piped dataframes).

Annonymous shorthand functions are also displayed as ‘aFunc’ in the Outline view.

ImageJ Plugin update:

  1. Improved the ‘Detach Images’ menu action
  2. Added an post activation action for detached views (‘Open All Images as Views’ action bugfix for Windows)
  3. Improved the layout action for orthogonal stack views (in detached views)
  4. Added an API method to invoke the ‘Open All Images as Views’ action
  5. The ImageJ macro action ‘setLocation’ will now change the size and location of detached views if available
  6. Fixed some minor bugs

For the R editor update add the following URL site to the Update Manager:

For ImageJ (if not already available) add:


Fixed OpenJDK Path for MacOSX – Allow Bio7 on Big Sur


Uploaded MacOSX version with corrected OpenJDK path

In the latest MacOSX release the path to the embedded Java OpenJDK was wrong (not a relative path). I uploaded a corrected version to sourceforge.

If you have already downloaded Bio7 you can simply correct the path in the Bio7.ini file (right-click, “Show Package Contents”, Path: “Contents/Eclipse”. Replace the vm path argument with the relative path to the embedded OpenJDK:


Fix – can’t run app because of permission in Big Sur

If you can’t open Bio7 after download even after the changes of the security settings try the following command-line recipe:

Solution which worked in the Terminal:

> sudo chmod -R 755 /Applications/

> sudo xattr -dr /Applications/

There is also a utility app available on Github to help with the MacOSX security settings, see:

Eclipse ImageJ Plugin Update Available


A new update of the Eclipse ImageJ plugin is available. This update comes with some nice editor improvements and now displays the image window information in the status line of Bio7 or (see screenshot below).

New in 1.53i (1.53.i25):

  • Updated ImageJ plugin to version 1.53i25
  • Improved the ImageJ macro editor speed. No more flickering editor markers if the files are bigger
  • Added a editor hoover to display editor hex color values and when selected the color and a hoover action to set the hex color with a dialog in place.
  • Added a sort and collapse action to the macro editor outline view.
  • Added the image information (which is normally displayed in the image window) to the Eclipse status line if a tab is selected or a stack/composite slider is moved.
  • Added an action to change the tab title color according to the color of the selected composite image channel.
  • Added a new color action for the new ImageJ message display method (tab title color and toolbar color)
  • Improved the outline redraw action for MacOSX

To update the ImageJ plugin in Bio7 open the Help->Install New Software dialog and select the ImageJ update site. If you have updated the ImageJ plugin before you can also execute the Help->Check for Updates action.