Confocal fluorescence microscopy

Laser scanning microscopy
Nipkow disk microscopy
Spinning Disk confocal microscopy

SODA suite


Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

Icy SODA logo



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

bleb dynamics


The purpose of the workflow is ....

First you need

need a thumbnail



Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

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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
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MorphoGraphX user interface



SOAX is an open source software tool to extract the centerlines, junctions and filament lengths of biopolymer networks in 2D and 3D images. It facilitates quantitative, reproducible and objective analysis of the image data. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments.

SOAX provides 3D visualization for exploring image data and visually checking results against the image. Quantitative analysis functions based on extracted networks are also implemented in SOAX, including spatial distribution, orientation, and curvature of filamentous structures. SOAX also provides interactive manual editing to further improve the extraction results, which can be saved in a file for archiving or further analysis. Useful for microtubules or actin filaments.

Observation: Depending on the operating system, the installation may or may not require Boost C++, ITK and VTK libraries. Windows has a standalone executable application without the need of those. 

snapshot microtubules soax

SGP-dec, A Scaled Gradient Projection method for 2D and 3D images deconvolution


A deconvolution component applicable to confocal and STED microscopy. The MATLAB function fo this package implements the SGP method for n-dimensional object deblurring with the option of boundary effects removal. Although this is a preliminary version, results seem to be good from their paper (Zanella et al 2013).

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Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment


The article describes how a FRAP experiment can be conducted and subsequently analyzed. This includes steps in ImageJ and subsequent normalization of the intensity data.

This is a qualitative analysis, and curve fitting is done using Excel. 

Requires "Template matching and Slice alignment plugin"

2D and 3D mitochondrial shape analysis and network properties


The original paper [publication 1] describes a method to analyze mitochondrial morphology in 2D and 3D and is based on previous work of the authors [publication 2].



The Huygens Software Suite consists of different image processing packages with functionalities that include deconvolution, interactive analysis, and volume visualization of 2D-3D multi-channel and time series images from fluorescence microscopes such as widefield, confocal, multi-photon, spinning disk, Array Detector, STED, and Light Sheet