Search Results for "microscopy"
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Showing 19 open source projects for "microscopy"
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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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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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ColorI-DT
A tool for the quantitative evaluation of differences in color images
...Contacts: Filippo Piccinini (emails: filippo.piccinini@irst.emr.it; f.piccinini@unibo.it) Repository: https://sourceforge.net/p/colori-dt/ How to cite us when using the tool: Filippo Piccinini et al. “Colori-DT: an open-source tool for the quantitative evaluation of differences in microscopy color images”. -
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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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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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MatQuantify
An image processing tool
...We analysed 217 microscopy images of untreated metaphase cells, 172 images of metaphase cells transfected with small interfering RNAs targeting the luciferase gene (as a negative control), and 230 images of metaphase cells depleted of CHC. Using the quantified data, we trained 23 supervised machine learning classificatio -
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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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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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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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scipion-doc
Scipion Documentation Project
This project contains documentation resources about the Scipion Framework for Image Processing in Electron Microscopy. -
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BrainImage
Two Photon Laser Microscopy
Two Photon Laser Microscopy Acquisition Code and image processing. -
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FluoJ
Fluorescence microscopy image analysis tool
Fluorescence microscopy became a common tool in cell and molecular biology. Image analysis of fluorescent molecules provides key information about the location, interactions, and dynamic behavior of target molecules. Usually user needs to recognize, characterize and classify particles, and in many cases to do statistical inferences from data collected. -
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...(XMIPP is a suite of image processing programs primarily aimed at obtaining the three-dimensional reconstruction of biological specimens from projection images obtained by transmission electron microscopy)
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Camscope is a multi-threaded program for acquiring and quantitatively analyzing images from an IIDC-compliant FireWire camera. It provides an integrated environment for performing quantitative video microscopy for teaching laboratories.
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A web-driven database for 2-D and 3-D images, specifically designed for (confocal) microscopy units, but applicable wherever groups of users collaborate with images.
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im-browser
MIB is a high-performance software package for image segmentation
Microscopy Image Browser (MIB) is a high-performance software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. Home page: http://mib.helsinki.fi -
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A framework for image analysis and data analysis, aimed towards microscopy and the needs of current research.
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