Search Results for "beta"
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Showing 34 open source projects for "beta"
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools... -
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ANDTool
Analysis Nuclei DAB (AND) Tool
Analysis Nuclei DAB (AND) Tool is a Graphical User Interface (GUI) to analyse microscopy images representing cells with nuclei stained using DAB dyes. The tool requires as input the original RGB images, and the FastRed, FastBlue, DAB channel, easily obtained using the Fiji function: "ImageJ" -> "Image" -> "Colour Deconvolution" -> "FastRed FastBlue DAB" Then, the tool first segment the nuclei using the FastBlue channel and the DAB channel, and then computes statistics by subdividing... -
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Marine Mammal Acoustic DCL
Advanced acoustic detection, classification and localization
Advanced detection, classification and localization (DCL) of marine mammals and passive acoustic monitoring (PAM). Code is being developed as Matlab routines, interfaces for Ishmael (http://www.bioacoustics.us/ishmael.html), and in other formats. -
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Microarray Integrator (MAI)
Microarray Integrator for heterogeneous human/mouse Affymetrix arrays
The Microarray Integrator is freely available programs to integrate heterogeneous Affymetrix microarrays for human and mouse. The cell-type-specific genes or condition-specific genes can be screened in the integrated microarrays by MAI result. -
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MAT-MECAS
Cell impedance analysis software.
MAT-MECAS is used for calculation of impedance parameters of a cell from recorded current responses elicited by bipolar voltage stimuli in a whole-cell patch-clamp experiment. The calculations are based on a FFT deconvolution procedure and on approximation of the reconstructed currents with a theoretical function. The impulse response of the signal path is necessary for the calculations. Read manual first! For testing MAT-MECAS we provide a sample data along with sample stimulation protocols. -
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BioRec:Bird Census field data annotation
Recognizing biological data from a notebook.
This project helps to digitize field data for a certain Bird Census method. Namely, bird census based on personal inspection or small (~10 km^2) regions with recording birds' position and behaviour on paper. This project makes it easy to annotate such field data and to make this data available for statistical analysis. -
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SoundRuler is a tool for acoustic analysis, graphing and teaching. It interactively recognizes and measures 35 temporal and spectral properties of each sound in a file. It also features several measurement, graphing and didactic modules.
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This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data
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RAFTS3
Rapid Alignment Free Tool for Sequences Similarity Search
RAFTS3 can perform high-speed protein search comparisons locally using a desktop computer or laptop. RAFTS3 performed searches many times faster than those with BLASTp against large protein databases such as NR and Pfam, with a small loss of sensitivity depending on the similarity degree of the sequences. RAFTS3 is a new alternative for fast comparison of protein sequences, genome annotation and biological data mining. Preprint: http://dx.doi.org/10.1101/055269 Precomputed databases... -
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OpenSegSPIM
OpenSegSPIM
OpenSegSPIM -
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of... -
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OpenFlux2 is an extended version of OpenFLUX (https://sourceforge.net/projects/openflux/) - the modern MATLAB-based modelling software for 13C flux analysis (MFA). The following features were implemented in OpenFLUX2, which were not present in original software: integrated support for calculation and analysis of parallel labeling experiments (PLE), extended statistical analysis of parameter estimation results, calculation of fluxes and measurements correlation, structural identifiability...
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QUDeX-MS
Hydrogen/deuterium exchange estimation for isotopic fine structure MS
Hydrogen-deuterium exchange coupled to mass spectrometry permits analysis of structural dynamics, stability, and molecular interactions of proteins. Resolving isotopic fine structure during mass spectrometry has been recently demonstrated to allow direct detection and quantification of deuterium incorporation distinct from peaks corresponding to non-deuterium incorporated natural abundance heavy isotopomers. Here, we present a graphical tool that allows for a rapid and automated estimation... -
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Online Signature Verification
Real time signature verification using MATLAB and C#
Online Signature Verification technology requires primarily a digitizing tablet and a special pen connected to the USB port of a computer. An individual can sign on the digitizing tablet using the special pen regardless of his signature size and position. The signature is characterized as pen-strokes consisting x-y coordinates and pressure with the data being stored in a signature database. Dynamic time warping (DTW) and quadratic discriminant analysis (QDA) is used to get results where the... -
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CS Miner
A tool for Navigating in Chemical Space
CS-Miner stands for Chemical Space Miner and is a software tool for navigating in chemical space of compound databases. It helps for deriving appropriate classification models and performing virtual screening. Download it via: http://csminer.com/csm/?p=7 A quick tutorial is available through: http://csminer.com/csm/?p=8 -
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FluxModules
Module Computation for Metabolic Networks
Genome Scale Metabolic Networks are complex systems, Modules help to break them down and hence ease understanding and algorithmic complexity. FluxModules is a toolbox with code for module detection and module visualization. -
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KYM is a MATLAB / GNU Octave set of functions that implements a wavelet-based automated procedure of quantification and characterization of biological signals. In particular it has been thought for the analysis of the oscillatory component of cytosolic calcium concentration time course.
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lonestar
A feature selection and classification algorithm based on L1 Norm SVM
A feature selection and classification algorithm. It is based on L1 Norm Support Vector Machine with t-test and Recursive Feature Elimination. -
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flNeuronTool
A Fast Light Neuron Tracing and Editor Tool
The flNeuronTool allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D interactive visualization-assisted environment, which is a powerful tool for analysis of complex neuronal images. -
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ISAD
Individual Synaptic Activity Detection (ISAD)
ISAD is a peak detection software that detects individual (pre-)synaptic activity in microscopy images from neuronal cultures transfected with pHluorin. It computes synaptic signals from automatically segmented regions of interest and detects peaks that represent vesicle fusion events, thus, pre-synaptic activity. ISAD is based on MWA, which is a continuous wavelet transform based algorithm that employs multiple wavelets and is published as: Sokoll, S., Tönnies, K., and Heine, M. Detection... -
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(AB)² Simulation
Simulation for Physics / Bilogics Systems
Supports flow Simulation for Physics and Meso-Compartimental Simulations for Biological Systems. Uses a Container-Flow based System. -
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A MATLAB package for wavelet analysis of circadian rhythms with both discrete (Daubechies) and continuous (Morlet) wavelets, as well as tools for batch processing of multiple time series, all accessible through a graphical user interface.
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PHACCS is a bioinformatic tool designed for a scientific public. It gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.
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This is a c-library that provides tools for advanced analysis of electrophysiological data. It features denoising, unsupervised classification, time-frequency analysis, phase-space analysis, neural networks, time-warping and more.
