Search Results for "microscope"
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Showing 28 open source projects for "microscope"
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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. ... -
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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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Scope
Software to run a two-photon microscope
Software to run a two-photon microscope -
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The Artificial SEM Image Generator (ARTIMAGEN) is a library that generates artificial scanning electron microscope (SEM) and helium-ion microscope images of various samples, including gold-on-carbon resolution sample, or some semiconductor features.
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White Blood Cell Differential Counter
Tally Cells as you view under microscope ⭐Please leave me a review
⭐Please leave me a review⭐ I live on feedback📬 This software allows staff to perform cell differentials using a keyboard. Simple $ useful! A new MSI installer has been created - an icon will appear on the desktop. ***************************************************************************** Don't be alarmed when installing the program. Windows will display an alert showing "unrecognized app", just click more info and then click run anyway to install WBC Diff counter. This warning... -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
This package of MATLAB routines with accompanying GUI allows scientific users to measure the 3D location of single molecules when using the double-helix point spread function (DH-PSF) widefield microscope. Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) - DH localization is performed through template matching and subsequent double Gaussian fitting - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions - Two spectral channels are registered by generating a locally-weighted quadratic mapping function from control point pairs -
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LER&LWR Calculator
Tool for line edge parameters calculation
Load a folder with images from raster electron microscope, choose necessary options and let the algorythm calculate the characteristics of the line. -
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F-Tracker3D
A software tool for tracking fluorescent cells in 3D
F-Tracker3D is acronym of "fluorescent cell tracker in three-dimensions". It is a software tool designed to track fluorescent cells using time-lapse z-stacks of images acquired with a confocal or light-sheet microscope. First, each single cell is tracked in 2D by using the maximum intensity projections of the z-stacks and CellTracker, the free open source software available at: www.celltracker.website. Then, the 3D track of each cell is obtained analysing the z-stacks and looking for the z-plane with the maximum intensity value for the different x-y positions previously determined. ... -
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experix laboratory control system
instrument control, data acquisition display and analysis
...Interfaces accessible via commands and scripts: file i/o modelled on stdio and stdlib; usb control and bulk transfers; socket operations; webcam; graphics via framebuffer. Applications (not all available yet for download) include: cell poker (like an atomic force microscope); tissue mechanical tester; fluorescence photobleaching; alternating laser excitation fluorescence; fluorescence intensity distribution analysis; iverilog simulation analysis. -
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SPIW - Scanning Probe Image Wizard
Scanning Probe Image Wizard - MATLAB Toolbox
SPIW is a MATLAB toolbox, for automated processing of scanning probe microscope images. Tools are applicable to all SPM images, but the main focus is on images with atomic or molecular resolution. SPIW is primarily a MATLAB toolbox with functions designed to be called in a user's own script. SPIW also has a very basic GUI for browsing and exporting images. For information on SPIW's performance see our publication ( http://dx.doi.org/10.1063/1.4827076 ) in the Review of Scientific Instruments. ... -
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ACCORD is a C library for composition of scanning electron or helium-ion microscope images with correction of drift. It produces significantly more accurate images than the traditional imaging techniques and also provides drift trajectories.
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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ANT.Gaussian
Quantum transport code based on Gaussian03/09
...Straightforwad use of ANT.G include the computation of the zero-bias conductance (or, alternatively, the electrical current under an applied bias voltage) of a variety of nanoscale systems such as molecular bridges or simply metallic atomic contacts as those created with scanning tunneling microscope or break junction techniques. 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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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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Java Virtual Petrographic Microscope
A virtual petrographic microscope for geologists
A free virtual petrographic microscope application which allows users to examine and explore minerals and rocks features. jVPM makes mineralogy to be easier to examine a thin section and to understand the characteristic properties for each mineral without a petrographic microscope, which is known to be very expensive. It is mainly addressed to students as a guide in individual or supervised laboratory work. -
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Ablator
A tool for automating laser ablations for neuroscience
Ablator is a suite of software that automates the microscopic detection of cell targets and also directs a 2-photon microscope to lesion these targets in arbitrary patterns for neuroscience research. See Hayes et al 2012 for an example of its usage (http://www.pnas.org/content/109/21/8286.abstract). -
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JohanneumSTM
Data logging and visualization in 2D and 3D for STMs.
This is a project we - ten students, 16 to 18 years old, and one teacher - are currently working on in the so called "Physik-Projektkurs" at school in which we build and program our own scanning tunneling microscope. This software is designed for DAQ systems by BMCM (we use the USB-AD16F), but it should not be too difficult to adapt it to foreign systems.It currently supports resolutions up to 1024x1024, visualization in 2D and 3D using colors from predefined gradients, export to PNG, CSV, OBJ and more! Requires at least .Net Framework 4.0, DirectX 9, optional: BMCM driver for your DAQ system -
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SURF-nanodots
Very basic computer vision program
...I'd like to clean it up and improve the back end design when time permits. See the wiki for known issues and more information. A computer vision program for analysis of magnetic data collected by a scanning probe microscope. Originated in summer 2007 as a collection of C compiled for Matlab (MEX) files and was eventually ported to a standalone C++ application with a GUI created in Qt. This program takes atomic and magnetic force microscope (AFM/MFM) image pairs as input and uses threshold segmentation to identify magnetic nanodots by intensity in the AFM image. ... -
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MATLAB GUI and code to map cell distribution around smooth spherical microcarriers beads from laser scanning confocal microscope images
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This toolkit allows complete control of a microscopy setup from Labview, Matlab, Scilab, Python, .Net, VB, IgorPro, Mathematica and more. Included is a standalone program for image acquisition and scripting control of a scientific microscope.
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A software to control a scanning ion conductance microscope, set up as described in http://www.blackwell-synergy.com/doi/abs/10.1046/j.1365-2818.2003.01248.x
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A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.
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This project provides a program for the capturing, editing and saving data from a SXM scanning tunneling microscope (http://sxm4.uni-muenster.de/stm-en/). The program is developed in C++ and based on a Qt library from TrollTech and libusb library.
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The virtual lab is a NASA-funded project to provide simulated instrumentation. ITG has developed a Virtual Microscope (Virtual SEM and LM) for viewing high-resolution, multi-dimensional image datasets. More info and data: http://virtual.itg.uiuc.edu
