A very time expensive process is the documentation of software you created yourself. I was finally able to update and improve the documentation for Bio7 and the embedded R “Graphical User Interface”. For the documentation this time i used Lyx to export the LaTeX document as HTML with the available eLyXer export module.
The R Graphical User Interface is documented here:
The documentation to transfer images and image data from ImageJ to R and vice versa can be found in this section:
I hope that this documentation will make it easier to explore the Bio7 R functionalities beside the flash videos i created.
In addition i created a new video (the first time i used Screencast-O-Matic) which explains how you can easily create a R plot with Bio7 using ImageJ as the default plot device or different available devices (PDF, SVG):
I was very unhappy with the default look and feel of my Rich Client Platform based on Eclipse 4.4 so i decided to work on a new custom CSS with gradients for Bio7. The nearly finished CSS (tested on Windows) is displayed below which corrects not only colours but also the different toolbar settings (background of the main toolbar and height of the view toolbars) to display e.g. the floating toolbar actions correctly without hiding other window elements.
There are still some minor bugs to correct. E.g. the Maximize, Minimize icons have to be resized to display the toolbar colour correctly.
In addition i was able to correct the alignment of the different Bio7 editor actions and i could even improve the integration of the JDT actions and hide unnecessary GUI elements for Bio7 (menu and toolbar – see screenshot below).
In the next release of Bio7 it will be possible to transfer opened ImageJ images from a tab to a detachable view. This action makes it possible to open several images side by side, detach images or translate them to a secondary monitor. In addition it is possible to nest several images in one detached window (see screenshot below).
At the moment i update the documentation for Bio7 using LaTeX and my preferred Latex editor Lyx to generate a HTML and PDF documentation with nice formatting options.
The first HTML results can be seen here and will be updated soon:
One of the features of the next release of Bio7 is the possibility to run an ImageJ simulation (dynamic image data) georeferenced on the 3D globe with – and this is new – a default transparent color (see image with running “Game of Life” below).
To run a simulation on a 3D globe with the current Bio7 version without a transparent color follow this tutorial:
Visualize dynamic images on the WorldWind globe