Category Archives: Bio7

Update the ImageJ Plugin for Bio7

19.05.2020

In Bio7 it is easy to update the Eclipse ImageJ plugin to the latest version. Open the main menu Help -> Install new Software dialog and add the following update site entry (see screenshot below) to install the update:

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

It might be recommended to externalize the default ImageJ plugin location (the plugins to extend ImageJ) in the Bio7 preferences (Preferences -> Preferences ImageJ -> Plugins Path) thus that the updates don’t overwrite the default location.

You could for example set the path to a local and remote Github repository to share the plugins with a team.

A change in the preferences will automatically update the ImageJ classpath at runtime (as in the ImageJ menu Help -> Refresh Menus).

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


Bio7 2.7 Bugfix Release for MacOSX

26.02.2018

Last week I released a new bugfix version of Bio7 which fixes some annoying bugs on MacOSX and updates some plugins.

  • Updated ImageJ to version 1.51v1
  • Improved the import of Java projects (No annoying dialog anymore)
  • Improved the execution of Shiny apps (No dialog when stopping the server)
  • Fixed several bugs and possible deadlocks regarding the swt_awt bridge and the OpenGL panel
  • Fixed a swt_awt key listener bug (ImageJ panel) to restore key events on the panel
  • Fixed a Mac bug in the R editor color dialog (hoover dialog of name R colors)
  • Huge fontsize for Swing (e.g., ImageJ dialogs) can be corrected for Retina displays (Bio7 ImageJ preferences – ‘-6’ for Retina displays fits well)
  • Bio7 editors and the Bio7 Workspace will be automatically saved before application shutdown

 

Download here

Improved ImageJ plugin

15.08.2016

Finally I had the time to improve the ImageJ plugin structure of the ‘Plugins’ view menu. Now the SWT menu structure of the plugin completely matches the AWT menu structure of  ImageJ (see screenshots below with some installed plugins).
Installed plugins, scripts and macros will be added to their defined menu path. Before this (current version) it was only possible to extend the SWT ‘Plugins’ menu and installed scripts and macros were only available if installed in the Bio7 main menu or by means of the ImageJ ‘Control Panel’.

Old:

beforeijmenu

New:

aftereijmenu

In addition I improved the image ‘Type’ menu to show checked menu items according to the opened image (see screenshot below).

checkmenu

Finally the ImageJ shortcuts will be mapped to the SWT menu if not used by the platform with a higher priority (see screenshot below).

shortcutsmenu

Some minor improvements will follow, too for the next update of the plugin which can be updated for Bio7 2.4 or any Eclipse environment soon.

 

 

Useful Eclipse Plugins for Bio7

21.02.2016

Here are some great Eclipse plugins useful in a scientific context which can be installed directly into Bio7 with the Eclipse Update-Manager of Bio7 (Help->Install New Software…).

Please note that you can also install the Eclipse Marketplace Client into Bio7 to install some of these plugins (a fancy interface to search for plugins):

EGit:
https://marketplace.eclipse.org/content/egit-git-team-provider
The powerful Git plugin to connect Bio7 with a Git repository.

TCF-Terminal:
http://marketplace.eclipse.org/content/tcf-terminals
A true native terminal with SSH,Telnet and Serial line support.

Eclipse CDT
https://marketplace.eclipse.org/content/eclipse-cdt-cc-development-tooling
C/C++ editor and development tooling.

Arduino C++ IDE:
https://marketplace.eclipse.org/content/arduino-c-ide
A great Arduino extension of the C++ editor of Eclipse.

PTP
https://eclipse.org/ptp/
An integrated development environment to support the development of parallel applications written in C, C++, and Fortran.

Photran
http://www.eclipse.org/photran/
An Integrated Development Environment and Refactoring Tool for Fortran

JSDT
https://eclipse.org/webtools/jsdt/
JavaScript editor and development tools

PyDev Editor:
https://marketplace.eclipse.org/content/pydev-python-ide-eclipse
A very powerful Python editor which can be used to execute Bio7 Jython and Python scripts instead of the Bio7 default editor. In addition Bio7 can use the PyDev editor to execute scripts running on the Bio7 Java classpath. If you open Jython/Python scripts with the PyDev editor the default Bio7 action will be visible to execute the scripts on the Bio7 classpath.

Groovy Editor:
https://marketplace.eclipse.org/content/groovy-eclipse-juno
A more powerful Groovy editor. Can also be used with the Bio7 classpath if scripts are opened with this editor instead of the default.

Jeeeyul’s Eclipse Themes
https://marketplace.eclipse.org/content/jeeeyuls-eclipse-themes
To install new styling themes into Bio7.

Eclipse Color Theme
https://marketplace.eclipse.org/content/eclipse-color-theme
If you need, e.g., a dark colored editor at night to rest your eyes.

Julia Editor
https://github.com/JuliaComputing/JuliaDT
A Julia editor in an early stage. But very promising.

Remote System Explorer
https://marketplace.eclipse.org/content/remote-system-explorer-ssh-telnet-ftp-and-dstore-protocols
A plugin to connect Bio7 with SSH, Telnet, FTP and DStore protocols.

This is a selection of a huge amount of available Eclipse plugins which can be installed into Bio7 to complement the default tools.