This tool allows to analyze morphological characteristics of complex roots. While for young roots the root system architecture can be analyzed automatically, this is often not possible for more developed roots. The tool is inspired by the Sholl analysis used in neuronal studies. The tool creates a binary mask and the Euclidean Distance Transform from the input image. It then allows to draw concentric circles around a base point and to extract measures on or within the circles. Instead of circles, which present the distance from the base point, horizontal lines can be used, which present the distance in the soil from the base-line. The following features are currently implemented:

  • The area of the root per distance/depth.
  • The number of border pixel per distance/depth, giving an idea of the surface in contact with the soil.
  • The maximum radius per distance/depth of a root, measured at the crossing points with the circles or lines.
  • The number of crossings of roots with the circles or lines.
  • The maximum distance to the left and the right from the vertical axis at crossing points with the circles or lines.
Concentric circles on the mask of a root, created by the Analyze Complex Roots Tool

Local Z Projector is an ImageJ2 plugin, available in Fiji, that can perform local-Z projection of a 3D stack, possibly over time, possibly very large.

LZP performs projection of a surface of interest on a 2D plane from a 3D image. It is a simple tool that focuses on usability and is designed to be adaptable to many different use cases and image quality.

  • It can work with 3D movies over time with multiple channels.
  • It can work with images much larger than available RAM out of the box.
  • It takes advantage of computers with multiple cores, and can be used in scripts.


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webKnossos is an open-source data sharing and annotation platform for tera-scale 2D and 3D image datasets.

The core features of webKnossos are:

  • fast 3D data streaming
  • share links to specific locations in the data
  • uniquely fast skeleton annotation (flight mode) and
  • efficient volume annotation
  • mesh rendering
  • collaboration and sharing tools

webKnossos facilitates image analysis workflows on multi-terabyte datasets, including visualization of raw and multi-modal microscopy data, distributed training data generation and proof-reading of automatic segmentation.

As a scientific resource, serves as a database for published image datasets including their annotations.





Viv is a JavaScript library providing utilities for rendering primary imaging data. Viv supports WebGL-based multi-channel rendering of both pyramidal and non-pyramidal images. The rendering components of Viv are provided as layers, facilitating image composition with existing layers and updating rendering properties within a reactive paradigm.

Rendering a pyramidal, multiplexed immunofluorescence OME-TIFF image of a human kidney using additive blending to render four image channels into a single RGB image in the client.


LaRoME = Label + Region Of Interest + Measure

Label image (aka Count Masks): An image in which pixels of an object have all the same value. Each object has a unique value.

Measurement image: An image in which pixels of an object have all the same value, corresponding to a measurement (Area, Angle, Mean...)

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