Category Archives: Uncategorized

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


The Road to OpenJDK 11

22.11.2018

it was a long road to the Java 11module system because a lot of bugs and settings had to be fixed for the next release of Bio7 which will be bundled with the OpenJDK as the default Java Runtime.

With Java 11 finally scaling of JavavFX, Swing and AWT components inside of Bio7 is supported on High DPI displays (SWT already supports this). However I have to make some more tests to remove the tiny drawing glitches if possible.

In additon with Java 11 SWT and JavaFX now support GTK 3 on Linux systems (see Ubuntu 18.10 screenshot below) still running on X11 which is default on Ubuntu (there are still some Wayland bugs which have to be resolved).

I already made some test exports on Linux and Windows and I think the next release (Bio7 3.0) will be available some time after the next Eclipse release which supports the Java 11 syntax completely.

 

Bio7 2.8 Released

30.05.2018

A new and improved release of Bio7 is available. The new Bio7 2.8 release comes with a plethora of new R features and bugfixes.

Release Notes:

General:

  • Updated Eclipse RCP to 4.7.3
  • Windows R update to version 3.5.0
  • ImageJ plugin updated to version 1.52d7
  • Added the ImageJ Edit perspective to the default opened perspectives
  • The R perspective is now selected as the opened perspective after startup of Bio7
  • Added an option to save all editors on close (default enabled on MacOSX)
  • Improved the main ‘Scripts’ menu to allow nested custom scripts in folders and subfolders which form new submenus
  • Improved the Table and R-Shell context scripts menu
  • Added some example scripts to the new scripts menu
  • Added an script to open the default script location in the OS file explorer
  • Simplified the different script locations (reduced to four locations in the Bio7 preferences)
  • Spatial import, export scripts moved to the main ‘Scripts’ and R-Shell script context menu (Deleted import, export script locations)

R:

  • Simplified the Bio7 R-Shell interface
  • Added a new view for some R templates
  • Code completion from loaded R packages can now be imported from the R-Shell or the R editor (both completions will be updated!)
  • Improved the reload code completion by only considering R functions (cleaner seperation of functions and datasets)
  • The updated R-Shell context menu can now dynamically be extended with custom scripts (updated dynamically). Folder and subfolders form new submenus.
  • Improved, bugfixed and extended the ‚Evaluate Line‘ action which was renamed to ‚Evaluate Line or Selection‘  action which now interprets selected R code, too.
  • Improved MacOSX ImageJ interaction (editor hoover focus)
  • Improved the call of the default plot device (quartz) in a native R connection on MacOSX (now default opened when, e.g., plotting, debugging, etc.)
  • Added a new menu to install Rserve for R > 3.5.0
  • New shutdown option to execute R code at shutdown (e.g., to save the current R workspace – a reload with the already existing startup option is possible, too!)
  • Improved the general error messages of the R-Shell view and the R editor evaluation. Now much simpler and printed cleaner!
  • Added an option to print the error stream of the Bio7 console to the R-Shell view (to the right output panel to get an output if the console is hidden!)
  • Fixed a bug with the shiny execution (removed annoying dialog)
  • Fixed many other bugs (unnecessary error messages, execution errors, MacOSX bugs, etc.)
  • R-Shell code completion improved (see editor code completion improvements below)
  • Removed the use of temporary files of the R-Shell and R editor code completion
  • Added an preference option to add arguments to the source command
  • Multiple selected R-Shell variables are now available in the R workspace (‘.r_shell_vars’ – a character vector) for the use in custom R scripts (e.g., to extend the R-Shell script context menu!)

R Editor:

  • Added a detection/quickfix function to install missing packages when a package load definition is in the editor file but the package is not installed

  • Added a quickfix to add a library definition when an unknown function is called (not defined and loaded but package with function is installed)
  • Added support for the the magrittr piping operator in code completion to autocomplete a given dataframe in the workspace (column completion)

  • Added code completion support for dataframes columns and rows, named list elements and named arrays (of arbitrary dimension)

  • Improved code completion to display current workspace variables
  • Classes of R objects are now displayed in the code completion context dialog
  • Editor variables and functions are now emphazised in code completion, too
  • Added a directory dialog to easily create a directory string for the editor file
  • Created new submenus for the organization of the context menu
  • Improved the hoover dialog (improved offset)
  • Improved the completion context of R objects (current workspace objects)
  • The styler package can now be used for an improved code formatting (requires UTF-8 Bio7 workspace on Windows – see preferences!)
  • Improved code completion for S3 and S4 objects (correctly display current cursor completion)

ImageJ:

  • Updated ImageJ plugin to version 1.52d7
  • Updated ImageJ2 libraries
  • Added new ImageJ macro functions to the code completion of the macro editor
  • Added the ImageJ Edit perspective to the default openend perspectives
  • Improved the editor hoover activation on MacOSX
  • Improved the ImageJ MacOSX touchpad resizing of the ImageJ panel

Java:

  • Updated JRE to 1.8.71
  • Improved the creation of Java projects and project imports (no annoying dialog anymore)
  • Improved the ‘Add Selected Libraries’ preference to add multiple Java libraries for dynamic compilation (e.g., to compile more embedded Eclipse library functions)
  • Now ImageJ2 libs have to be added to the dynamic compilation libraries for compilation (removed as default libraries)
  • Added a key shortcut (STRG + ‚+‘) to increase the SceneBuilder panel (2x)

Download and Installation:

Windows:

Just download the *.zip distribution file from https://bio7.org and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.

Linux:

Download and extract the installation file from https://bio7.org.
For Linux you have to install R and Rserve (see Rserve installation below!).

MacOSX:

Download and extract the installation file from https://bio7.org.

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition for MacOSX you have to install R and Rserve (see below!).

Linux and MacOSX Rserve (compiled for cooperative mode) installation:

To install Rserve open the R shell and then execute the menu action “Options -> Install Rserve (coop. mode) for R …” for different R versions. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!). In cooperative mode only one connection at a time is allowed (which we want for this Desktop appl.) and all subsequent connections share the same namespace (default on Windows)!

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the R-Shell context menu “Packages” action:

R-Shell context menu->Packages->Install_Default_R_Packages

Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.