Software developed at INEB

The MIQuant is an opensource software developed with the objective of automating the infarct extension estimation in animal models (mice). In the specific operation of the MIQuant software the user is asked to provide input seed points for the left ventricle’s lumen and the healthy heart tissue areas, sequentially.

Cell File Analyzer
Cell File Analyzer is an automatic tool to detect cell files, the main structure in plant roots. The obtained cell file detection enables the automatic extraction of important data on the plant development stage and of characterisitics for individual cells, reducing in more than 90% the time required for the analysis.

LCFs - Local Convergence Filters
LCFs allow the detection of cell nuclei and joint detection of cytoplasm without the use of image segmentation. LCFs are local interest point detectors based on the direction of the image gradient and not magnitude, making them robust to image contrast variations.


Equipment specific software

Leica LAS AF Lite
LAS AF Lite is the free version software from the Leica LAS AF developed by Leica Microsystems CMS GmbH. This software allows you to read and export -lif files generated by the SP5 Leica Confocal.
You can downloaded from here

IDEAS software integrates imaging and population statistics for the data obtained in the ImageStream. With this software populations can be defined by discriminating them with different features and statistically analyzed. Analysis scheme ideas can be saved and used as a template for batch processing future experiments.

LabSpec 5
LabSpec 5 software is a fully configured data acquisition and analysis software designed for HORIBA Scientific’s range of Raman spectrometers and microscopes. It enables a full range of experiment types including single spectrum acquisition, multidimensional spectral array acquisition (including time profiles, Z (depth) profiles, temperature profiles, XY maps, XZ and YZ slices, and XYZ datacubes), video image capture and automated multiwell interrogation. Many commonly used data analysis and processing routines are also available, including peak labelling and fitting, smoothing, noise reduction, baseline subtraction, linear and non-linear filtering and direct classical least squares modelling.

Vevo Software
This softwate from VisualSonics facilitates the real time visualization and measurement of anatomy and the quantification of physiology in adult, neo-natal and (in utero) embryonic mice. Data and measurements can be exported and summarized to standard formats for offline statistical analysis and calculation as well as use in presentations reports and publications.

Image analysis software

ImageJ is an open source software for image processing and analysis developed at the National Institutes of Health. It can read images in different formats including TIFF, PNG, GIF, JPEG, BMP, DICOM, FITS, as well as raw formats. It supports standard image processing and also allows the creation of plugins for new analysis.
FIJI is just ImageJ. FIJI includes a large amount of plugins from ImageJ focused on assisting research in life sciences.

Open Microscopy Enviroment - OME
OMERO is a client-server software for visualisation, management and analysis of biological microscope images.

GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. The Octave language is quite similar to Matlab so that most programs are easily portable.

MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. MATLAB can be used for a wide range of applications, including signal processing and communications, image and video processing, control systems, test and measurement, computational finance, and computational biology.

Gimp2 is a powerful image editor that it is freely available.

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