Flat field correction

Protein Array Analyzer for ImageJ


Protein array is used to analyze protein expressions by screening simultaneously several protein-molecule interactions such as protein-protein and protein-DNA interactions. In most cases, the detection of interactions leads to an image containing numerous lines of spots that will be analyzed by comparing tables of intensity values. To describe the observed different patterns of expression, users generally show histograms with the original associated images [1]. The “Protein Array Analyzer” gives a friendly way to exploit this type of analysis, thus allowing quantification, image modeling and comparative analysis of patterns.

The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot Analyzer, [2], [3] a graphically interfaced tool that greatly simplifying analysis of dot arrays.



Acquiarium is open source software (GPL) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation.

It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

Acquiarium functionalities diagram

Spark Stitcher


Reconstruct big images from overlapping tiled images on a Spark cluster.

The code is based on the Stitching plugin for Fiji


ANTs: Advanced Normalization Tools


ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.

Image Registration

Diffeomorphisms: SyN, Independent Evaluation: Klein, Murphy, Template Construction (2004)(2010), Similarity Metrics, Multivariate registration, Multiple modality analysis and statistical bias

Image Segmentation

Atropos Multivar-EM Segmentation (link), Multi-atlas methods (link) and JLF, Bias Correction (link), DiReCT cortical thickness (link), DiReCT in chimpanzees


Advanced Normalization Tools



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

Illumination correction method



Image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy. Tools included:

  • 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time.
  • Optimal filament segmentation of 2D images. 
  • Curvature filters for image filtering, denoising, and restoration. 
  • Image naturalization for image enhancement based on gradient statistics of natural-scence images. 
  • Tool for automatically send and distribute jobs on clusters and get back the results.
  • Multi-region image segmentation of 2D and 3D images without needing to know the number of regions beforehand. 
  • Squassh for globally optimal segmentation of piecewise constant regions in 2D and 3D images and for object-based co-localization analysis. 
  • Tool for inferring spatial interactions between patterns of objects in images or between coordinates read from a file.
  • Tool for robust, histogram-based background subtraction well suited to correct for inhomogeneous illumination artifacts.
  • A tool to estimate the Point-Spread Function of the microscopy out of 2D fluorescence images.
  • A tool to measure the 3D Point-Spread Function of a confocal microscope from an image stack.
  • Addition of synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. 
  • Convolution of an image with a Bessel function in order to simulate imaging with a microscope. 
  • A utility to detect bright spots in images and estimate their center. 
  • A utility to create manual segmentations to be used as ground truth to test and benchmark automatic segmentation algorithms.
  • A tool for replacing one color in an image with another color.
has topic

Uneven illumination correction


Illumination correction is often important for both accurate segmentation and for intensity measurements. This example shows how the CorrectIlluminationCalculate and CorrectIlluminationApply modules are used to compensate for the non-uniformities in illumination often present in microscopy images.

need a thumbnail

Background Subtractor


Histogram-based background subtractor for ImageJ.

The implemented algorithm is based on the assumption that, compared to the background region, object (foreground) regions are small. The plugin builds local histograms and assumes the most occuring intensity to be part of the background.



CorrectIlluminationCalculate calculates an illumination function that is used to correct uneven illumination/lighting/shading or to reduce uneven background in images.

has topic

Local Normalization (ImageJ)

need a thumbnail