Tools

BioVoxxel Tools

BioVoxxel provides many free tools to the image analysis community in form of Fiji plugins, scripts and macros. Those tools are already widely cited in scientific literature. Fiji (and specifically ImageJ as basis of Fiji) is one of the most used image analysis software in life sciences. It is free and open source!

can be downloaded here.

To install all BioVoxxel plugins at once you can:

Download the following Configuration File
Drag and drop the downloaded file onto the Fiji main window
In the script editor window which will then open just press the [Run] button (lower left corner)
As soon as it is ready with the setup it shows you the updater window
Just press the [Apply Changes] button.
As soon as the updating is done it will tell you to restart Fiji

Alternatively you can install the plugins separately by checking out their documentation page links below.

See short descriptions of the main tool boxes and libraries with further links to source code and documentation by extending the sections below:

BioVoxxel 3D Box

Re-writings of many known BioVoxxel Toolbox functions as well as completely new plugins for 2D and 3D image processing and analysis in one place. All functions are heavily GPU-based via the fabulous CLIJ2 library. Segmentation output is mainly based on labels (intensity coding of objects) instead of ROIs, making it more flexible, and compatible with other image processing tools.

Featured Tool is the Voronoi Threshold Labeler (VTL) for 2D/3D object segmentation.

Code on Github

Documentation

Please cite the tool

Short video on some featured functionalities (talk from the I2K conference 2022)

BioVoxxel Toolbox

The BioVoxxel Toolbox is an established ImageJ/Fiji suite which contains plugins and some macros dealing with image filtering, image segmentation and binary image processing as well as various analysis tools, such as cluster analysis and comparative object counting and measurements.

Code on Github

Documentation

Please cite the tool

BioVoxxel Figure Tools

The BioVoxxel Figure tools should make it easier to create high quality publication figure grade images out of Fiji directly into an SVG vector graphics file which can then be used in Inkscape for further figure creation.

Code on Github

Documentation

Please cite the tool

Excel Functions

The Excel macro extensions for ImageJ and Fiji are meant to make saving results tables as .xlsx worksheet files and tabs in ImageJ and Fiji easily accessible on various different levels.

Maven Dependency

<dependency>
    <groupId>de.biovoxxel</groupId>
    <artifactId>excel.macro.extensions</artifactId>
    <version>3.2.1</version>
</dependency>

Code on Gitlab

Maven Repository

Documentation