Search Results for "quantitative"
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Showing 13 open source projects for "quantitative"
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CometAnalyser
CometAnalyser, for quantitative comet assay analysis.
Description: Comet assay provides an easy solution to estimate DNA damage in single cells through microscopy assessment. To obtain reproducible and reliable quantitative data, we developed an easy-to-use tool named CometAnalyser. CometAnalyser is an open-source deep-learning tool designed for the analysis of both fluorescent and silver-stained wide-field microscopy images. Once the comets are segmented and classified, several intensity/morphological features are automatically exported as a spreadsheet file. ... -
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AnaSP
AnaSP, a MATLAB software suite to ANAlyse SPheroids' features
Today, more and more biological laboratories use 3D cell cultures and tissues growth in vitro as model of in vivo tumours and metastasis. However, a lack of methods for quantitative analysis, limits the usage of spheroids as model for routine experiments. AnaSP is a suite tool for automatic analysis of morphological parameters of spheroids starting by brightfield images manually acquired with a standard widefield microscope. AnaSP is distributed as an open source software tool, and its modular architecture and graphical user interface make it attractive also for non-Computer Scientist people, and suitable for both high content screenings and occasional spheroid-based experiments. ... -
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Artifact GeoMorph Toolbox 3D 3.1
A toolbox for 3DGM shape analysis of archaeological artifacts
...As such, the toolbox contains an automated item and semi-landmarks positioning procedure and the fundamental statistical analyses and procedures to allow the processing and analysis of the data. It is designed to be easy to use and straightforward with a simple graphical user interface. Furthermore, it provides direct, quantitative and objective results to answer common archaeological research questions with regards to artifact shape variability. -
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Spheroid_segmentation
Deep learning networks for spheroid segmentation
...The code provides the trained networks based on Vgg16, Vgg19, ResNet18, and ResNet50 ready to be used for segmentation purposes. It also provides Matlab functions ready to be used to train new networks, segment new images, and measure the quality of the training using different quantitative parameters. -
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5
DSeg software
A MATLAB program to segment filamentous bacteria and hyphae structures
The analysis of microscopy image has been the basis to our current understanding of the cellular growth and morphogenesis. The quantitative evaluation of morphological changes in the biological processes is therefore important to characterize cell structures. Here we present an image analysis tool DSeg to overcome the difficulties in finding complicated elongated cell shapes by using time-lapse data and cell morphological constraints. A fast binary level-set based algorithm is implemented for extracting object contour and refining shapes. ... -
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GVAR
The GVAR Toolbox 1.1 is designed for the purpose of GVAR modelling.
...L.Vanessa Smith's project Exploring International Economic Linkages Using a Global Model, the GVAR Toolbox 1.1 is the second release of a collection of MatLab procedures with an Excel-based interface, designed for the purpose of GVAR modelling. The GVAR modelling approach provides a general yet practical global modelling framework for the quantitative analysis of the relative importance of different shocks and channels of transmission mechanisms. This makes it a suitable tool for policy analysis, although it has been used in a number of other contexts, including analysing credit risk and evaluating the UK entry into the Euro. The GVAR Toolbox 1.1 is primarily tailored to policy analysis and forecasting. -
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MicroMos
To automatically obtain mosaics of partially overlapping images.
...It was designed for stitching microscopy images, but thanks to the many parameters available it works also for other types of images. For more details, please, read: a) F. Piccinini, M. Pierini, E. Lucarelli, A. Bevilacqua, Semi-quantitative monitoring of confluence of adherent mesenchymal stromal cells on calcium-phosphate granules by using widefield microscopy images. Journal of Materials Science: Materials in Medicine, 25(10):2395-2410, October 2014. 2) F. Piccinini, A. Bevilacqua, E. Lucarelli, Automated image mosaics by non-automated light microscopes: the MicroMos software tool. ... -
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JAABA
The Janelia Automated Animal Behavior Annotator
The Janelia Automatic Animal Behavior Annotator (JAABA) is a machine learning-based system that enables researchers to automatically compute interpretable, quantitative statistics describing video of behaving animals. Through our system, users encode their intuition about the structure of behavior by labeling the behavior of the animal, e.g. walking, grooming, or following, in a small set of video frames. JAABA uses machine learning techniques to convert these manual labels into behavior detectors that can then be used to automatically classify the behaviors of animals in large data sets with high throughput. ... -
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IBEX_MDA
An open infrastructure software to facilitate radiomics research.
...IBEX software package was developed using the MATLAB and C/C++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. -
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Qi - Quantitative Imaging (PIV and more)
A collection of MATLAB tools for PIV, PTV, particle sizing, and more.
Qi is a collection of MATLAB tools for the quantitative analysis of flow field images. Our Particle Image Velocimetry (PIV) tool, prana, implements a Robust Phase Correlation kernel for PIV analysis, and now includes Particle Tracking Velocimetry and sizing tools. Tools for pressure calculation, proper orthogonal decomposition (POD), and 3d imaging are under development. -
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FinMetrics - MATLAB based, open source/open architecture quantitative portfolio management environment.
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DoseLab is a set of software programs for quantitative comparison of measured and computed radiation dose distributions. It is written in the Matlab programming language and is easily extensible to more general applications in radiation physics.
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A toolbox for quantitative morphometric analysis of early development in spherical embryos, such as Xenopus laevis (African Clawed Frog). The toolbox is developed for Matlab 6.5 and higher and combines C-Mex code with Matlab functions.
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