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
ImageJ
![application biologique imageJ](https://www.quantacell.com/wp-content/uploads/2019/10/logo-imagej-150x150.png)
Free software for image analysis. It allows to create made-to-measure plug-ins.
Icy
![software programmation Icy imaging](https://www.quantacell.com/wp-content/uploads/2019/10/Icy_imaging-150x150.png)
Free software for image analysis. More elegant than ImageJ with many automatizations.
Cell Profiler and Cell Profiler Analyst
![cellprofiler_quantacell](https://www.quantacell.com/wp-content/uploads/2019/12/cp_logo-300x75.png)
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
![Ilastik](https://www.quantacell.com/wp-content/uploads/2019/12/ilastik-logo.png)
Advantage: allows to do 3D segmentation based on deep-learning
Programming languages adapted to biomedical data analysis
Python
![python_data_sciences](https://www.quantacell.com/wp-content/uploads/2019/12/QuantaCell-Python-logo-notext.svg-150x150.png)
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](https://www.quantacell.com/wp-content/uploads/2019/10/logo-malab-150x150.png)
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](https://www.quantacell.com/wp-content/uploads/2019/10/logo-r-150x150.png)
Statistics-dedicated language.
Advantage: 100% free adapted for data analysis. Used for scientific publications.
C# .Net
![C++ language](https://www.quantacell.com/wp-content/uploads/2019/10/logo-microsoft-150x150.png)
Advantage: well adapted for general graphic applications. A huge users community. A lot of tools for graphic interface, network and databases.
Java
![java programmation](https://www.quantacell.com/wp-content/uploads/2019/10/logo-java-150x150.png)
Advantage: well adapted for general graphic applications. A huge users community. A lot of tools for graphic interface, network and databases.
C/C++
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.
CUDA
![data treatment](https://www.quantacell.com/wp-content/uploads/2019/10/logo-nvidia-150x150.png)
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.
SQL et MyPhP/MySQL
![bases de données](https://www.quantacell.com/wp-content/uploads/2019/10/logo-mysql-150x150.png)
Database-dedicated language and a simple and free administration interface.
QuantaCell, Hôpital Saint Eloi, IRMB
80 av Augustin Fliche
34090 Montpellier, France
Contact
+33 (0) 9 83 33 81 90