Search Results for "microscopy"
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Showing 43 open source projects for "microscopy"
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Quality Management SoftwareisoTracker Quality Management is a popular cloud-based quality management software (QMS) that is used by small to medium sized businesses on a worldwide basis. It helps to manage ISO 9001, ISO 13485, ISO 22000, ISO 17025, ISO 14001 systems...plus many similar other systems. It also conforms to the requirements of 21 CFR Part 11.
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Junie, the AI coding agent by JetBrainsJunie is an AI-powered coding agent developed by JetBrains designed to enhance developer productivity by integrating directly into popular IDEs such as IntelliJ IDEA, PyCharm, and Android Studio. It supports developers by assisting with code completion, testing, and inspections, ensuring code quality and reducing debugging time.
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Gwyddion
Scanning probe microscopy data visualisation and analysis
A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis. -
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computem
Transmission Electron Microscope Image Simulation
These programs calculate high resolution conventional and scanning transmission electron microscope (CTEM, STEM) images of thin specimens from first principles using the multislice method for electrons in the energy range of approximately 60 keV to 1000 keV. The fundamental theory and usage are described in "Advanced Computing in Electron Microscopy" (Springer 2020) and Acta Cryst. A72 (2016) p. 1 by Earl J. Kirkland. Please refer to these for the theory of calculation and how to use these programs. computem uses a GUI and the temsim group uses a command line interface. The user is assumed to have some understanding of optics, Fourier transforms, electron microscopy and computer skills at the graduate or advanced undergraduate level. ... -
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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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Gwyscope
Open hardware SPM controller with advanced sampling support.
Gwyscope is a low cost, open hardware, Digital Signal Processor (DSP) suitable for Scanning Probe Microscopy measurements, focusing on demonstrating the concept of adaptive scanning, general XYZ data acquisition and statistical data processing on the controller level. More details can be found in: M. Valtr et al., Scanning Probe Microscopy controller with advanced sampling support, HardwareX, Volume 15, e00451 https://www.hardware-x.com/article/S2468-0672(23)00058-5/fulltext It is based on a low cost FPGA board Red Pitaya and additional high bit depth AD and DA converters. ... -
ERP Software To Simplify Your ManufacturingGlobal Shop Solutions AI-integrated ERP software provides the applications needed to deliver a quality part on time, every time from quote to cash and everything in between, including shop management, scheduling, inventory, accounting, quality control, CRM and 25 more.
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TomoJ
ImageJ plugin to perform Electron Tomography
...reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy."Messaoudi C et al -
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GSvit
Fast FDTD solver with graphics card support
Fast FDTD solver with graphics card support. Optimized for nanoscale optics - scanning near field optical microscopy, rough surface scattering and solar cells. Uses CUDA environment for graphics card operation. -
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GXSM
Scanning Probe Microscopy Controller and Data Visualization Software
GXSM -- Gnome X Scanning Microscopy: A multi-channel image and vector-probe data acquisition and visualization system designed for SPM techniques (STM,AFM..), but also SPA-LEED/LEED/LEEM data analysis. A plug-in interface allows any user add-on data-processing and special hardware and instrument support. Latest: NC-AFM and related explorative methods as SQDM can be configured. -
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AtomicJ
Application for analysis of AFM data
AtomicJ is an application for analysis of force microscopy recordings, including images and force curves. It allows for fast and reliable processing of single force curves and force maps, providing estimation of the mechanical properties of the sample. AtomicJ supports a wide range of contact mechanics models, including the models for blunt tips, the corrections for the effect of finite sample thickness, models of adhesive contact and models of spherical indentation of hyperelastic material. ... -
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coDDMaker
distributions and co-distribution 2D signal analysis
coDDMaker is a MATLAB® App Designer's software program for the guided analysis of the distributions and co-distribution of marker pairs in 2D image. -
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DDMaker
Local Distribution Density Map Maker
DDMaker perform local density analysis and generates pseudocolor maps of the spatial distribution of imaged cellular structures in 2D images, starting from either RGB color, grey level or binary images. DDMaker local density analysis permit to selectively denoise the signal, visualize and quantify its distribution and threshold the image basing on local density. -
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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 the sample in three regions according to the FastRed channel: a dark-red ROI, a light-pink ROI and a white ROI. ... -
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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. Optionally, also the extraction of nucleus features and a double-scale analysis of orientation can be performed. ... -
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UmUTracker
A MATLAB program for 2D particle tracking or 3D DHM based tracking.
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing long video sequences acquired by either light microscopy or digital holography microscopy (DHM). Our program finds the 2D particle center position using an isosceles triangle transform and the axial position by a fast implementation of Rayleigh-Sommerfeld numerical reconstruction algorithm using a one dimensional radial intensity profile. *Updates v1.1: 2017/11/21- Bug fix & Blob detection functions. ... -
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Qu is a MATLAB toolbox for the visualization and analysis of N-dimensional datasets targeted to the field of biomedical imaging. It supports several microscopy image formats and offers a plugin mechanism and a consistent API for easy extension.
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sdmixer
A tool for 2D/ 3D multi-color super resolution microscopy
The open source software sdmixer reconstructs a TIFF image from a single molecule localization data set. The spectral demixing option allows multi color super resolution microscopy. sdmixer supports multipage TIFF images and is able to process large 3D data sets. Further features are 2D/3D convolution, histogram based contrast enhancement and nearest neighbor analysis. -
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MicroMos
To automatically obtain mosaics of partially overlapping images.
MicroMos is an open-source software tool written in MATLAB (The MathWorks, Inc., Massachusetts, USA), for automatically obtaining mosaics of partially overlapped images, also manually acquired. 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. ... -
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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
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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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BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
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ANT.Gaussian
Quantum transport code based on Gaussian03/09
...The use of ANT.G may also be naturally extended to the computation of scanning tunneling spectroscopy and the simulation of scanning tunneling and electrostatic force microscopy. -
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xmipp
Image processing suite for Electron Microscopy
XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es -
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scipion-xmipp
Image processing framework to integrate EM software packages.
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. -
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
From Amat et al., Nature Methods, 2014*: "The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. 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... -
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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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GIIAF Microscopy Library
The GIIAF Microscopy Library, that uses customised OMERO software
This project incorporates a suite of tools that aim to allow researchers within Griffith's Imaging and Image Analysis Facility (GIIAF) to efficiently and effectively provide secure, centralised, web-accessible data storage, management and manipulation. The open-source Java-based OMERO software was customised to provide most of the features of this project.
