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.


has function

MSER based on implementation in imglib2 provided as an interactive GUI tool for spot detection in 2/3/4D images.


QuantiFish is a quantification program intended for measuring fluorescence in images of zebrafish, although use with images of other specimens is possible. This package is geared towards analysis of fluorescent infection models. The software is designed to automate processing of images of single fish, and outputs results as a .csv file. Alongside measures of total fluorescence above a threshold, this package also introduces several measures for dissemination and distribution of fluorescence throughout the specimen.

QuantiFish User Interface

Histology Topography Cytometry Analysis Toolbox (histoCAT) is a package to visualize and analyse multiplexed image cytometry data interactively. It can also export data in.fcs data for further analysis using  a specialized cytometry sofwtare such as Flowjo. 

It can be run as a compiled standalone or from matlab.