Image Analysis Scripts

In the process of developing or implementing new microscopy assays, we have written numerous image analysis and representation scripts for Matlab or ImageJ/FIJI. Below is a selection. Codes have been written for specific applications and image types, but may have generic value for other microscopy applications. Feel free to contact me for scripts or more information. 


A FIJI plugin for mapping anatomical information onto microtome-cut brain slices. For every image of a brain slice, the algorithm performs a coarse congealing-based registration to a library of pre-annotated reference slices. A subset of optimally matching reference slices is then used for refined, elastic registration. (> Download Package)

Reference: Barbier et al. (2017). Bioinformatics.


Blebbed Nuclei Detector. Plugin for accurate detection of dysmorphic, and in particular blebbed nuclei based on two-tier segmentation and dynamic programming. Integrates both detection and classification tools. (> Download Package)

Reference: Verschuuren et al. (2016), Plos One 12(1): e0170688 


A FIJI plugin for fusing bi-directionally recorded microscopic image volumes via 3D rigid transformations. The method is compatible with image data sets from all optical sectioning microscopes and does not rely on fiducial markers for image registration. (> Download Package)

Reference: Detrez et al. (2016). Bioinformatics 32, p. 3691-3693.


Script that automatically tracks nuclei and measures their signal intensity fluctuations through time. Specifically conceived to detect and quantify spontaneous nuclear rupture events in migrating cells. It runs on images that contain either one single or two nuclear markers. 

Reference: Robijns et al. (2016), Scientific Reports 6, 30325(1-11)


Script for quantifying mitochondrial morphology and potential in C. elegans or human cells. Works by selective enhancement and multi-scale Laplacian filtering to effectively segment mitochondria, followed by derivation of shape, texture and intensity metrics. Can be extended by incorporating an additional cell staining, to express metrics in relative terms.

Reference: Sieprath et al. (2016), AAEC 219, p. 149-177.


In Silico Cytometric Decomposition Analysis. Flexible high content analysis to measure descriptive features about cell and nucleus as well as intracellular objects. Demands a nuclear channel to facilitate segmentation of individual nuclei and conditional expansion to segment cellular regions of influence. A variety of visualization and correction tools is available. 

Reference: De Vos et al. (2010), Cytometry 77:64


A fully automated method for quantifying neuron morphology and density of neurite networks, in neuronal cultures. The image analysis pipeline consists of a multi-tier approach in which the somas are segmented by adaptive region growing using nuclei as seeds, and the neurites are delineated by a combination of various intensity and edge detection algorithms. 

Reference: Pani et al. (2014), Cytometry 85:188


Script for extracting pancellular signal fluctuations through time from cellular calcium or ROS markers (eg. FLUO4-AM resp. CMDCFDA). No additional stains are required for cell segmentation. The analysis was recently expanded to also cater for analysis of mitochondrial morphology and signals.

ReferenceStaljanssens et al. (2011), Peptides 34:219


This script performs quantitative colocalisation analysis between two channels, including standard intensity-based methods (Overlap, Pearson, ICA) and a novel object-based method based on absolute overlap between segmented (binarized) channels. 

Reference: Verdoodt et al. (2012), Cell Biol Int 36:1251


Mobility analysis of telomeres (or blob-like structures) in time acquisitions of human cell nuclei. Nuclear mobility can be corrected for by rigid registration. An adaptive thresholding algorithm localizes objects in 3D. Automated tracking of particles is done by an iterative size-modulated nearest neighbour algorithm. Includes interactive visualization and correction options. 

Reference: De Vos et al. (2010), J Microscopy 238:254


This script converts a dual color acquisition of e.g. a ratiometric dye/probe into an HSB image whereby the hue represents the ratio of both fluorescence channels and the value the combined intensity of both channels. This representation allows distinguishing significant ratiometric differences in relevant regions, i.e. where the signals are sufficiently high. 

Reference: Back et al. (2012), Free Radical Biol Med 52:850

Wound Closure

This script automatically measures the cell-free area from a wound healing assay in multi-well format. It is conceived to work with timelapse recordings, acquired in transmission or fluorescence mode (e.g. signals from DII or Calcein). Includes manual inspection and correction action tools. 

Reference: Van Lancker et al., Exp Biol Med 2018