Search Results for "level set method"
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Showing 10 open source projects for "level set method"
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xfemm
Cross platform electromagnetics finite element analyisis based on FEMM
...Development of xfemm now takes place on Github here: https://github.com/REOptimize-Systems/xfemm xfemm is a refactoring of the core algorithms of the popular Windows-only FEMM (Finite Element Method Magnetics, www.femm.info) to use only the standard template library and therefore be cross-platform. The codes can be used as a library, standalone executables, or through the advanced Matlab/Octave interface, which uses direct data exchange at the memory level rather than the original FEMM ActiveX or file-based interface, for much improved communication speed. ... -
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Orbit Determination Toolbox (ODTBX)
Advanced mission simulation and analysis tool
...ODTBX functions and utilities are combined in a flexible architecture that allows for modular development of navigation algorithms and simulations. The core ODTBX functionality is realized through a set of estimation commands that incorporate Monte Carlo data simulation, linear covariance analysis, and measurement processing at a generic level. -
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ReViSP
ReViSP, a 3D volume rendering MATLAB tool for multicellular spheroids
...Computer Methods and Programs in Biomedicine, 118(2):95–106, 2015. (b) F. Piccinini, et al., Single-image based methods used for non-invasive volume estimation of cancer spheroids: a practical assessing approach based on entry-level equipment. Computer Methods and Programs in Biomedicine, 135:51-60, 2016. -
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adcptools
Set of functions to process acoustic Doppler current profiler data
adcptools is a set of Matlab functions to post-process acoustic Doppler current profiler data. It consists of several low-level function to read out data files and several functions to process data from repeat transect measurements, moored turbulence measurements and horizontal ADCP deployments. -
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DSeg software
A MATLAB program to segment filamentous bacteria and hyphae 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. The software is implemented in MATLAB for segmenting and tracking of cell contours from various microscopy systems. Video instructions: https://www.youtube.com/embed/qMbM0shkk7A?rel Lastest updates: 20190930 DSeg: A dynamic segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures,(2018). ... -
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EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence. Please download EigenMS.zip file (latest version). Latest version uploaded in October 2017 has a bugfix for single treatment group normalization. Rescaling has been omitted from 2015. EigenMS utilizes SVD to detect bias trends in the data and eliminates them.
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected Square method (OMES), McLanhlan Based Substitution Correlation (MCBASC), Direct-coupling analysis (DCA) and logR. ... -
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K-Level 2.0 [revised]
An application of leveling network adjustment using Matlab
This is an application of leveling network adjustment based on Matlab. The method used in this application is least square adjustment. User can enter the leveling data directly or by reading a text file. -
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CupidTool
Cupid: simultaneous reconstruction of miRNA-target and ceRNA networks
Chiu et. al., Genome Research 2014 Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. We showed that our integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines. Cupid is implemented in 3 steps: Step 1: re-evaluate candidate miRNA binding sites in 3’ UTRs, as inferred by TargetScan, miRanda and PITA by integrating their scores, location in the 3’ UTR, and cross-species conservation. ... -
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CRUMp
A probabilistic prediction system of protein phosphorylation sites
CRUMp is based on a kernel-based learning method called Classification Relevance Units Machine (CRUM). Given an input set of protein sequences in FASTA format, the system outputs the position, residue type (S, T, or Y), and the estimated probability of each tested site being phosphorylatable. Latest downloadable files: - crump-0.2.0.tar.gz: CRUMp GNU Octave package - crump-0.2.0.zip: CRUMp MATLAB script - crumptestset.fasta: A testing dataset in FASTA format.
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