Category Archives: Uncategorized

Fixed OpenJDK Path for MacOSX – Allow Bio7 on Big Sur

02.05.2021

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:

-vm
../MacOS/jdk/Contents/Home/lib/libjli.dylib

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:

https://stackoverflow.com/questions/64842819/cant-run-app-because-of-permission-in-big-sur

Solution which worked in the Terminal:

> sudo chmod -R 755 /Applications/Bio7.app

> sudo xattr -dr com.apple.quarantine /Applications/Bio7.app

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

https://github.com/wynioux/macOS-GateKeeper-Helper

Eclipse ImageJ Plugin Update Available

05.03.2021

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.

ImageJ Plugin Update

27.02.2020

A new ImageJ plugin update is available which can be installed into Bio7 3.1 (as an update) or Eclipse. Several new features are available.

Release Notes

  • Updated ImageJ plugin to version 1.52u28
  • Added a new thumbnail action to the context menu of the ‘Navigator’ view to open image and LUT files of a selected directory.
  • LUT’s can now be displayed (preview) in the ‘Thumbnails’ view. The selected LUT will be applied on the current supported ImageJ image (grayscale).
  • The Image info is now displayed as a popup in the ‘Thumbnails’ view (if you hoover over an item).
  • Added a ‘Detach All Images’ action (menu ‘Window’) to transfer all opened tab images to a view (which can be moved and arranged like a separate window)
  • Improved dark theme for AWT on Windows, MacOSX and Linux.
  • Added custom text properties to allow future dark themes or disable dark theme color schemes.
  • Improved the canvas layout for HighDPI displays on Windows.
  • Added new default macro editor templates.
  • Improved the default AWT fonts (using OS fonts).
  • Fixed a SWT memory bug not releasing native children of image tabs.
  • ImageJ Plugin Perspective with opened Thumbnail view (Windows)

Installation

To install the plugin the latest Java >=8 is required (only for Eclipse) and an installation of Eclipse or Bio7 3.1 (which is already bundled with OpenJDK 13.0.2).

The plugin can be installed from the Eclipse Marketplace:

https://marketplace.eclipse.org/content/imagej-plugin

As an alternative (and update for Bio7 3.1) open the Help->Install new Software dialog and add the following update site (see screenshot below):

https://bio7.github.io/imagej/

Then install the following features (see screenshot below):

Note for Bio7 3.1:

When installing the update for Bio7 3.1 don’t forget to recalculate the JDT Project Classpath for Java Projects (Context Menu ‘Project Explorer’ -> Fix Project Classpath) for the updated ImageJ plugin location.

Bio7 MacOSX And Windows Update Available

19.04.2019

I created an update for MacOSX and Windows which can be easily installed with the Update Manager of Bio7. This update fixes some bugs (which affects Windows and MacOSX only), adds two new scripts in the R-Shell view and updates the ImageJ plugin to version 1.52o33.

Before you update Bio7 make sure that you make a backup of possible installed scripts and ImageJ plugins in the default script and ImageJ plugin location because these two plugins and their preferences will be updated (it might be a good practice to externalize these locations in the Bio7 preferences for updates in the future).

Installation:

1. Add the update sites below to the Update Manager (Help->Install New Software)

2. Add the URL (Location) of the Update Site (see below).

3. Close the Update Manager and then check for Updates (Help->Check for Updates).

4. Select Bio7 and confirm all licenses and unavailable certificates during installation.

Update Sites for Windows and MacOSX:

Windows: https://bio7.org/update/win/repository
Mac: https://bio7.org/update/mac/repository