Search Results for "fluorescence"
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Showing 17 open source projects for "fluorescence"
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Stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra. Graphical user interface (GUI) and batch processing capabilities provided.
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
...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 for: (a) segmenting z-stacks of fluorescence images; (b) reconstructing the 3D surface of the aggregates and estimating several features (including the volume). ReViMS is written in MATLAB (The MathWorks, Inc., Massachusetts, USA). It is an open-source tool and the source code is freely available at: http://sourceforge.net/p/revims Requirements: MATLAB R2017b and Image Processing Toolbox 10.1 or later versions. -
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Tempico software
Software to control and analyze Tausand Tempico timing data
Tempico Software is designed to control the Tausand Tempico TP1004 and TP1204 devices, a time-to-digital converter that captures temporal differences from a common start signal across multiple channels. The software generates histograms from captured data, supports lifetime measurements via single-photon correlation (SPC), and displays real-time graphs with adjustable fitting options. It includes a 'Counts Estimation' panel to estimate count rates per channel over time, and a 'Time Stamping'... -
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XISMuS
X-Ray Imaging Software for Multiple Samples
...IMPORTANT FIXES in respect to base v2.0.0 version: v.2.5.0 introduces the Differential Attenuation and Cube Viewer utilities, and migrates user database to *.json files v2.4.3 fixes a with K element in the fit-approx method v2.4.3 fixes and issue where saving plots with fit-approx or a auto-wizard could freeze the software v2.4.2 introduces Image Viewer to Mosaic v2.4.1 fixes an issue in merging H5 or EDF datasets with Mosaic Full changelog at https://linssab.github.io/history X-Ray Fluorescence Imaging Software for Multiple Samples is an open source software to manipulate and study macro-X-Ray Fluorescence (MA-XRF) datasets. XISMuS also works as a sample management tool, where you can easily change between datasets (samples) and compare, cross-interact and normalize them. -
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MORPHEUS for Fiji
A tool for unbiased and reproducible cell morphometry in Fiji/ImageJ2
MORPHEUS is a Fiji/ImageJ2 plugin for the automated evaluation of cell morphometry from cell cultures images acquired by fluorescence microscopy. Specifically, MORPHEUS works with sampling distributions to learn—in an unsupervised manner and by a non-parametric approach—how to recognize the cells suitable for subsequent analysis. Afterwards, the algorithm performs the evaluation of the most relevant cell-shape descriptors over the full set of detected cells. -
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Spectral-SpecPro
Spectral - software for manipulating optical spectroscopy data
Spectral-SpecPro helps with the manipulation of optical spectroscopy data. Spectral takes files produced by Jasco instruments (uv-vis absorbance, fluorescence, circular dichroism readings as a function of wavelength, temperature, or time) and facilitates basic operations such as unit conversion (CD spectra), conversion into the format taken by CDPro (estimation of secondary structure; CD spectra), scatter correction (absorbance spectra), smoothing, re-sampling of the x-axis, and generic combination (sum, product, average, standard deviation) of multiple curves. ... -
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MDA
Molecular Dynamics Analyzer (MDA)
MDA is a 3D single-particle tracking software that explicitly addresses fluorescence microscopy experiments deep in living specimens. It is capable of minimizing the systematic error that occurs with astigmatism-based 3D techniques owing to the aberrations induced by the refractive index mismatch. In contrast to existing techniques, the method determines the aberration directly from the acquired 2D image stream by exploiting the inherent particle movement and the redundancy introduced by the astigmatism. ... -
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
...We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities." ... -
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FABS
Fluorescence and absorption spectroscopy made easy
...FABS was designed with students in mind, as a way to help high schoolers and undergraduates learn about spectroscopy without paying for expensive equipment and software. Accompanying this software is a hardware design, which can be used as a bare-bones spectrometer that will provide quantitative absorption and fluorescence emission spectra at an extremely low cost. It uses only materials that many people can find around their home. -
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flow visualization toolbox
matlab 2D image processing GUI toolbox for flow visualization
A general flow visualization Matlab toolbox for image processing of some common planar/surface visualization techniques from PLIF (Planar laser induce fluorescence) for tracer distribution, BOS (background oriented Schlieren) for density, TSLC (Temperature sensitive liquid crystal) for thermal and PSP (Pressure sensitive paint) pressure distribution measurement. This work is part of author's PhD study, under Dr S. Zhong @ the University of Manchester's supervision, guidance and support. ... -
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NanocalcFX
Open Source Data Evaluation Software
NanocalcFX is a free and open source evaluation software for a simple yet comfortable solution to deal with thousands of transport kinetics measured with a fluorescence microscope or similar kinetics. Data can be imported from CSV or Excel files or using the dedicated image stack analyser (NISA). You can get sample data at the nanocalcFX homepage. Note that nanocalcFX is currently in a beta state. -
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LAVA for AFM
Lloyd's Algorithm-based Volumetric Analysis for AFM Images
...As the name implies, LAVA uses Lloyd's Algorithm, also known as k-means sorting, to identify a small set of volumes representative of the actual distribution of particle in the image. Although developed for determining feature volume, LAVA is also completely compatible with other types of image analysis, such as fluorescence intensity. Work is in progress to provide three-channel functionality, allowing comparison of relative intensity of red, green, and blue channels in multi-color images. -
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This is the prototype version of software for robust detecting and segmentation of cell nuclei in 3D fluorescence labeled microscopy images. First release coming soon...
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NOSE is a package for simulation of linear and non-linear optical and infrared spectra, including absorption, fluorescence, circular dichroism, pump-probe, photon echo and other.
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Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
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global-processing
https://github.com/seanwarren/global-processing/wiki
Package for processing Fluorescence Lifetime Imaging Microscopy (FLIM) Data
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