Software Development
IMAGE PLATFORM
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- Image Analysis and Quantification Support Service
- Analysis Workstation (Room B37)
- Analysis Workstation (Room B02)
Responsible:
Mikel Ariz: mikelariz@unav.es
Phone: +34 948 194 700 Ext. 1043
Biomedical and medical image analysis
We develop software tools tailored to each user, adapted to each specific problem.
![img-desarrollo-software-plataforma-imagen](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-desarrollo-software-plataforma-imagen.jpg)
Most applications are developed as macros or plugins for Fiji/ImageJ. It is a free software platform, which allows the user to make use of our applications from any computer and perform their own image analysis and quantifications.
![img-intro-herramientas-analisis-imagen](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-intro-herramientas-analisis-imagen.jpg)
We work with different image modalities
![img-cores-tma](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-cores-tma.jpg)
Automatic extraction of individual cores from full TMA images.
Individual cores are extracted as single images for further processing by other Fiji plugins.
![img-dab-cuantificacion](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-dab-cuantificacion.jpg)
Detection and quantification of DAB immunostaining. Quantification of positive area to tissue area ratio. Possibility of manual removal of regions (necrotic areas, folds, etc.).
![img-deteccion-cuantificacion-celulas-individuales](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-deteccion-cuantificacion-celulas-individuales.jpg)
Detection and classification of single cells in H&E DAB images. Sorting and counting of DAB positive or negative cells.
![img-analisis-celularidad-tejido-adiposo](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-analisis-celularidad-tejido-adiposo.jpg)
Adiposoft: automated software for the analysis of cellularity in white adipose tissue in histological sections. Segmentation of individual adipocytes. Morphological quantification of each adipocyte to obtain the complete distribution.
![img-colonias-cultivo-celular](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-colonias-cultivo-celular.jpg)
Analysis of colony formation assays in cell culture plates. Adaptation of the "ColonyArea" plugin by Guzman et al. 2014. Semi-automatic detection of individual wells, segmentation and quantification of area and number of colonies formed in each well.
![img-ondulacion-elastina-arterias](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-ondulacion-elastina-arterias.jpg)
Analysis of elastin waviness in arteries. Automatic detection of the artery lumen, elastin ripples in the inner contour, approximation of a contour without ripples and calculation of the length ratio between both contours: rippled (green) vs. approximation without ripples (red).
![img-cuantificacion-tejido-fibrotico](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-cuantificacion-tejido-fibrotico.jpg)
Quantification of fibrotic tissue by Sirius Red staining. Automatic detection of tissue and regions with positive Syrian Red staining. Calculation of ratio of positive area vs. total tissue area.
![img-deteccion-fibras-musculares](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-deteccion-fibras-musculares.jpg)
Automatic detection, classification and quantification of muscle fibers in immunofluorescence images.
![img-segmentacion-aorta](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-segmentacion-aorta.jpg)
Quantification of angiogenic vessel growth from a segment of the aorta.
![img-poblaciones-celulares-inmunofluorescencia](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-poblaciones-celulares-inmunofluorescencia.jpg)
Quantification of cell populations in multiplex fluorescence imaging.
![img-nets-fluorescencia](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-nets-fluorescencia.jpg)
Detection of NETs in multiplex fluorescence imaging by marker localization.
![img-segmentacion-automatica-tumores](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-segmentacion-automatica-tumores.jpg)
Automatic segmentation of different regions of tumor tissue using machine learning techniques.
![img-microcontact-printing](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-microcontact-printing.jpg)
Detection of tumor cells on a deposited pattern by microcontact printing
![img-proteinas-nucleo-microplasma](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-proteinas-nucleo-microplasma.jpg)
3D quantification of protein expression in nucleus and cytoplasm in cell cultures.
![img-estructuras-oseas](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-estructuras-oseas.jpg)
3D segmentation and quantification of bone structures in CT images. Quantification of bone volume and density, and histomorphological parameters in the case of trabecular bone structures.
![img-cuantificacion-3d-pulmonar](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-cuantificacion-3d-pulmonar.jpg)
3D segmentation and quantification of lungs and airways in CT images. Quantification of mean lung volume and intensity, with characterization of the degree of emphysema or infection.
![img-estructuras-cerebrales](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-estructuras-cerebrales.jpg)
Segmentation and quantification of brain structures in MRI images.
![img-tracking-2d-celulas](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-tracking-2d-celulas.jpg)
Segmentation and 2D tracking of cells in microfluidic devices. Calculation of the track of each cell along the sequence and quantification of cell migration parameters.
![img-celulas-3d-alta-resolucion](/.imaging/dmsChain/dam/cima/imagenes/plataformas/imagen/img-celulas-3d-alta-resolucion.jpg)
3D segmentation and characterization of cells by high resolution microscopy. Morphological quantification and detection of filopodia in different cell phenotypes.