Software programmation for biological applications

When available software tools on the market do not fit to expectations, it is possible to create a new tool, a new software, a new script, a new program. We present here imaging softwares highly configurable and the programming languages adapted to imaging fields, data analysis and visualization.

Imaging software for microscopy


application biologique imageJ

Free software for image analysis. It allows to create made-to-measure plug-ins.


software programmation Icy imaging

Free software for image analysis. More elegant than ImageJ with many automatizations.

Cell Profiler and Cell Profiler Analyst


CellProfiler is a free and open source software designed to enable automatic measurement of phenotypes from thousands of images


Advantage: Allows you to develop advanced pipelines and apply them to large batches of images


Ilastik is a free and user-friendly open source software for image classification and segmentation. No prior image processing experience is required to run the software.  

Advantage: allows to do 3D segmentation based on deep-learning

Programming languages adapted to biomedical data analysis



Many purpose scientific programming language. Highly used for deep learning and statistics. It can be used for website back-ends to include scientific mechanisms

Advantage: almost all deep learning algorithms are available in Python. It is a great choice for QuantaCell. QT in Python can be easily included. 

Matlab (MathWorks)

matlab analyse de données biomédicales

Scientific programming language very complete.

Advantage: because of a lot of scientific functions, time of programming is very short. Specifically adapted to scripts writing without elaborated graphic interface.

R language 

r software programmation

Statistics-dedicated language.

Advantage: 100% free adapted for data analysis. Used for scientific publications.

C# .Net

C++ language

Advantage: well adapted for general graphic applications. A huge users community. A lot of tools for graphic interface, network and databases.


java programmation

Advantage: well adapted for general graphic applications. A huge users community. A lot of tools for graphic interface, network and databases.


Old and efficient. Additional libraries.

  • QT : used for elaborated graphic interfaces. Multiplatform and Free
  • OpenCV : image analysis and data mining-dedicated library. Multiplatform and Free.

Advantage: fast, reliable, multiplatform.


data treatment

Programming of graphic chips for very fast executions.

Advantage: adapted to big image treatment algorithms. It allows to save 30% of time compared to a C++ algorithm equivalent on processor.


bases de données

Database-dedicated language and a simple and free administration interface.

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