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

Bio7 3.3 Released

22.04.2021

I released a new version of Bio7. Bio7 3.3 includes a plethora of new features, improvements and bugfixes.

Screenshot: Bio7 MacOSX R ImageJ Analysis perspective

For those who don’t know Bio7. The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis.

It also contains a feature complete development environment for R with an advanced R editor, R developer tools and interfaces to perform scientific image analysis with R and the embedded ImageJ application.

New features:

General

  • Bio7 3.3 is based on Eclipse 4.19
  • AdoptJDK updated to Java version 16
  • JavaScript bundled with AdoptJDK (Nashorn)
  • Updated JavaFX libraries (version 16) bundled with AdoptJDK
  • Bundled with R 4.0.5 (Windows only!)
  • Updated Java libraries (Groovy, JavaScript, etc.)
  • Added some Eclipse default themes (e.g. “System” theme for Linux)
  • Improved the themes, wording and some visuals
  • Improved the Bio7 file wizard in the toolbar
  • Added a sort and collapse actions to some editors outline view

R

  • New “Attached Packages” view which displays datasets and function of packages. Datasets can directly be loaded

  • The “Load” and “Save” action in the R-Shell View can now load and save files in different selected formats (the command will be loaded into the textfield of the shell). A selection of extensions is not necessary anymore. The R history can be saved and loaded, too. This action is also available in the R editor to create file templates
  • Improved the speed of the R editor markers (new Eclipse API)
  • R editor markers don’t flicker anymore
  • Improved the general R editor speed
  • Added an Outline view action to sort and collapse the tree view of variables and functions
  • Improved the code completion. Now by default opens after a prefix length of 2 but can now also be opened at any time (new Eclipse API)
  • Updated Rserve to version 1.8.7
  • Created an easy to use Rserve install method action (R-Shell view->Context menu->Rserve->Install Rserve)

Java

  • Added dynamic compilation support for Java 15 (support for “Raw String Literals” to avoid the “quoting hell” of embedded commands in strings)
  • Added a new Java interface API method to execute R code from Java in a job with plotting and intermediate plotting support

Groovy

  • Updated Groovy interpreter
  • Groovy editor now supports “Raw String Literals”

JavaScript

  • Bundled a Nashorn JavaScript engine with AdoptJDK 16
  • Added an interpret toolbar action when the Eclipse GenericEditor is installed and a JavaScript file is opened with the editor

ImageJ

  • Updated the ImageJ plugin to version 1.53j18
  • Huge improvements since the last Bio7 release (this plugin can be continuously updated within Bio7), see release notes: https://github.com/Bio7/EclipseImageJ1Plugin
  • Improved the close method for all plugins
  • Detached views can now be closed by name in a macro, etc.
  • Selected Composite Image channels are now displayed colored in the status line of Bio7
  • Added the latest ImageJ macro templates

R & ImageJ

  • Improved the image classification plugin (bundled with the application) and visuals
  • Classified images can now be post-processed with an ImageJ macro for object recognition or particle counting, etc.

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 Java AdoptJDK, R, Rserve and works out of the box.

Linux:

Download and extract the installation file from https://bio7.org.
Bio7 comes bundled with Java (AdoptJDK).
For Linux you have to install R and Rserve.
To install Rserve start R (after installation) in the Bio7 console and execute in the context menu of the R-Shell view:
Rserve->Install Rserve

MacOSX:

Download and extract the installation file from https://bio7.org.
Bio7 comes bundled with Java (AdoptJDK).
To install Rserve start (R after installation) in the Bio7 console and execute in the context menu of the R-Shell view:
Rserve->Install Rserve

Note for the Rserve installation:

The install action installs  a special Rserve version compiled for cooperative mode from Github. In cooperative mode only one connection at a time is allowed (which we want for this Desktop apl.) and all subsequent connections share the same namespace (default on Windows)!

MacOSX startup notes:

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, Sierra, Mojave and Big Sur:

First try to open the app with the context menu to allow the execution. If that won’t work try the following:

Yosemite: Open an app from an unidentified developer

Sierra: Open an app from an unidentified developer

Moave and Sierra: How to fix “Application” is damaged and can’t be opened error in macOS Mojave and High Sierra.

Bio7 Documentation

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

A plethora of Bio7 videotutorials for an introduction can be found on YouTube.

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.

Bio7 3.2 Released

20.11.2020

A new version of Bio7 is available. This update comes with a plethora of new features, improvements and bugfixes.

Bio7 3.2 Dark theme enabled using the spatstat package examples and plots.

For those who don’t know Bio7. The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis.

It also contains a feature complete development environment for R with an advanced R editor, R developer tools and interfaces to perform scientific image analysis with R and the embedded ImageJ application.

New and Noteworthy

General:

  • Bio7 3.2 RCP (Rich Client Platform) built upon Eclipse 4.17
  • Bundled with AdoptOpenJDK 14.0.2 and JavaFX 15
  • Bundled with R 4.0.3 (Windows only!)
  • Added an image classification plugin for supervised and unsupervised image classification (using R and ImageJ – see R-Shell view context menu “Image Classification”). For an overview and details, see: https://github.com/Bio7/Bio7_Classification

Image Classification plugin (Dark Theme enabled)

  • Menus and scrollbars are now dark on Windows, too
  • Improved the dynamic script menus. Nested folders can be hidden for complex Java plugins (see image classification plugin).
  • Updated several Java libraries (Groovy, POI, etc.)
  • Improved several view layouts (showing scrollbars if necessary)
  • Changed all SWT ExpandBars to CTabFolders to improve the display when the dark theme is selected
  • Added more default fast wizards actions to the toolbar menu (to create Bio7 projects with files in one action)

Opened fast wizard menu (Dark Theme enabled)

  • Added new API methods (e.g., an R script job interface)
  • Enabled the recognition of Eclipse supported ASCII control characters in the console (see preferences)
  • Improved the compilation of pure LaTeX files without the necessity to run Rserve
  • Improved the dark theme on Windows, Linux and MacOSX

ImageJ

  • Updated the ImageJ plugin to version 1.53g34 (see ImageJ release notes)
  • Improved the visual interface for debugging
  • The main view menu can now be extended dynamically from plugins
  • ImageJ macros updated
  • Toolbar menus improved
  • Converted the ImageJ toolbar menus to SWT to display the dark theme
  • Converted several ImageJ context menus to SWT (recognizable on HighDPI, Linux GTK)
  • For all changes since the last release, see: https://github.com/Bio7/EclipseImageJ1Plugin

R

  • Updated the embedded R application on Windows
  • The R plugin can now be updated individually
  • Added a new ‘Load Packages’ table to display installed R packages and if updates available (selected packages can be updated in this view, too)

Load Packages tab (Dark Theme)

  • Added a grammar rule for raw string literals to the R editor (thanks to Bart Kiers)
  • Added a database preference to store the XML database profile file in a different (secret) location.
  • Fixed some minor R-Shell bugs

R + ImageJ

  • Added an option to transfer ImageJ ROI groups or special ROI names as class signatures to R (ROI Manager transfer actions in the Image-Methods view)
  • Improved the ROI stack transfer for virtual stacks (to load and transfer disk resident image stacks)
  • Improved several functions for the new image classification plugin

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, Sierra, Mojave and Big Sur:

First try to open the app with the context menu to allow the execution. If that won’t work try the following:

Yosemite: Open an app from an unidentified developer

Sierra: Open an app from an unidentified developer

Moave and Sierra: How to fix “Application” is damaged and can’t be opened error in macOS Mojave and High Sierra.

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 ‘Native R’ console in the ‘Console’ view and then execute the view menu action “Options -> Install Rserve (coop. mode) for R …” for different R versions (SSL 1.1 version for Linux Ubuntu > 19.10).
This will download and 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!):

How to install Rserve for Linux and MacOSX: https://youtu.be/tF7HbRBRIF

In cooperative mode only one connection at a time is allowed (which we want for this Desktop apl.) and all subsequent connections share the same namespace (default on Windows)!

Bio7 Documentation

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

A plethora of Bio7 videotutorials for an introduction can be found on YouTube.