Search Results for "fluorescence"
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Showing 19 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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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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CliMA Land
Everything within the Land model
CliMA Land is a next generation Land Surface Model (LSM) designed to use the broadly available remote sensing data as well as ground-based flux measurements. CliMA Land is a highly modular platform to promote research at different scales from tissue to organ, whole plant, and ecosystem. Therefore, we deliver CliMA Land via a patch of packages (also referred to as sub-modules) to reduce the time used to initialize a research project. As a result, the repository is more a collection of... -
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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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Chooch
Determine f'' and f' from X-ray fluorescence spectra
A program for deriving anomalous-scattering factors from X-ray fluorescence spectra. -
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MatQuantify
An image processing tool
MatQuantify, written in MATLAB, detects both large-scale and subtle structural changes in the spindle or DNA and can be used to statistically compare the effects of different treatments. MatQuantify can quantify various physical properties extracted from fluorescence microscopy images, such as area, lengths of various components, perimeter, eccentricity, fractal dimension, satellite objects and orientation. It can also measure textual properties including entropy, intensities and the standard deviation of intensities. Using MatQuantify, we studied the effect of knocking down the protein clathrin heavy chain (CHC) on the mitotic spindle. ... -
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The software can be used to co-localize spots in 2 or 3 movies containing single molecule fluorescence data with surface immobilized molecules. If movies are taken on more than 1 camera, offset files can be made and then used to warp one of the movies (or two of the movies if working with three). Time traces for identified spot triples and pairs can be subsequently viewed. The software was created at the University of Colorado Boulder by James Goodrich, with the help of Abigail Horn and Jennifer Kugel.
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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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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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XAS Data manipulation for 100-element fluorescence detector at SSRL
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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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