A collection is a software that encapsulate a set of bioimage components and/or workflows.


Bio Image Analyst

The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy.


Bio Image Analyst

By combining multiple image alignment and tracing into one program, Reconstruct (TM) allows images to be processed more efficiently. Tracing can be done directly on the transformed images and alignments can be asily modified. Reconstruct (TM) was developed from years of experience working with high magnification serial section images of brain tissue. (Extracted from User Manual)

NET - Network Extraction Tool

Bio Image Analyst

The ultimate goal of the NET framework is to make images of networks processable by computers. Therefore we want to have a pixel based image as input, as output we want a representation of the network visible in the image that retains as much information about the original network as possible. NET achives this by first segmenting the image and then vectorizing the network and then extracting information. The information we extract is


Bio Image Analyst

The invention comprises a software tool, NeuronMetrics, which functions as a set of modules that run in the open-source program ImageJ. NeuronMetrics features a novel method for estimating neural “branch number” (a measure of the axonal complexity) from two-dimensional images. In addition, the tool features a novel method for modeling neural structure in large “gaps” that result from image artifacts.



MorphoGraphX is a free Linux application for the visualization and analysis of 3D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 3D live-imaged confocal data sets.

The main research interests adressed by MorphoGraphX are:

  • Shape extraction
  • Growth analysis
  • Signal quantification
  • Protein localization


CIDRE is a retrospective illumination correction method for optical microscopy. It is designed to correct collections of images by building a model of the illumination distortion directly from the image data. Larger image collections provide more robust corrections. Details of the method are described in

K. Smith, Y. Li, F. Ficcinini, G. Csucs, A. Bevilacqua, and P. Horvath
CIDRE: An Illumination Correction Method for Optical Microscopy, Nature Methods 12(5), 2015, doi:10.1038/NMETH.3323