114 results

MIB2 is an update package for segmentation of multi-dimensional (2D-4D) microscopy datasets

With MIB2 you can analyse, segment and visualize various multidimensional datasets from both light and electron microscopy. MIB2 is completely rewritten to follow MVC architecture and brings

MIB is a package for segmentation of multi-dimensional (2D-4D) microscopy datasets

herehttp://se.mathworks.com/matlabcentral/fileexchange/63402-microscopy-image-browser-2--mib2-With MIB you can analyse, segment and visualize various multidimensional datasets from both light and electron microscopy. See more further details and tutorials on MIB website

Toolbox for the ceQPM method

. "Computationally Enhanced Quantitative Phase Microscopy Reveals Autonomous Oscillations in Mammalian Cell Growth." bioRxiv (2019): 631119.The image processing pipeline includes:1. load the experiment information2

Automated analysis of electron microscopy images (PC and Mac versions available.)

. Chem. Soc. 2014, 136, 7603 doi: 10.1021/ja503509kHigh-Throughput, Algorithmic Determination of Nanoparticle Structure from Electron Microscopy ImagesChristine R. Laramy, Keith A. Brown, Matthew N

Functions for reading and writing image files and STAR files for electron microscopy

This directory contains m-functions for reading and writing files used in electron microscopy and 3D reconstruction. The file formats those used by the IMAGIC software package (Image Science GmbH

This is a synthetic image generation tool that can create realistic Pap-smear images

This is a simulator able to procedurally create realistic bright-field microscopy images depicting Pap-smears. The principles used in the simulation are described in the paper "Simulation of

This code Find out the best infocus image from a image stack using Tamura coefficient.

This matlab code implements Tamura Coefficient to find out the best infocus image in the stack of the images.The stack of the microscopy has many images but one of the image is the best

neuropoly/axonseg

version 3.0.0.0

by Aldo Zaimi

AxonSeg is a GUI that performs axon and myelin segmentation on histology images.

Segment axon and myelin from microscopy data. Written in Matlab. The compiled versions are also available for those who do not have the necessary processing toolboxes.

Correct nonlinear drift distortions in scanning probe images.

This collection of scripts is intended to correct nonlinear drift distortions in images recorded using any scanning probe microscopy technique (where there is a slow and a fast scan direction). It

Automatic thresholding of fluorescence microscopy images in microfluidics to determine platelet coverage and aggregate size distribution.

DIPimage

version 3.0

by Cris Luengo

Toolbox for Quantitative Image Analysis

GUI for detection of fluorescent cells in In-Resin Fluorescence sections

Matlab GUI for automated detection of fluorescent cells in In-Resin Fluorescence sections for Integrated Light and Electron Microscopy

MATLAB code for a Graphic User Interface dedicated to automatically count and quantify dendritic spines from fluorescence microscopy images

MATLAB code for a Graphic User Interface dedicated to automatically count and quantify dendritic spines from fluorescence microscopy images. It has been tested with .oib files from

Automatic detection of nanoparticles using hyperspectral microscopy and machine learning

Automatic detection of nanoparticles using hyperspectral microscopyNanoparticles are used extensively as biomedical imaging probes and potential therapeutic agents. As new particles are developed and

Remove spatial frequencies beyond the optical cutoff and perform physically accurate interpolation.

. Filtering the spatial frequencies beyond the optical cutoff provides simple yet effective means of reducing noise. Since microscopy data is band-limited, padding in frequency domain provides accurate

The M-file is to calculate the g-ratio for Scanning or Transmission Electronic Microscopy.

The algorithm presented here segments retinal blood vessels with a high degree of accuracy.

of Fungal Hyphae in Macroscopic Microscopy Image Stacks." arXiv preprint arXiv:1704.02356 (2017).Saranya, M., and A. Grace Selvarani. "Fundus Image Screening for Diabetic Retinopathy." Indian Journal

A collection of matlab scripts for processing and analysing scentific data (images, time-domain measurements, and spectra).

This is a collection of the matlab tools that I have developed to process and analyse my data. Most of my experimental work is with atomic force microscopy, so these scripts are typically used for

the TREES toolbox: edit, generate, visualise and analyse neuronal trees

for a quantitative description of dendritic and axonal morphology.The TREES toolbox provides:Tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic

Reads and imports Asylum Research ARDF files to Matlab structures for force curve analysis.

For atomic force microscopy force curve analysis within Matlab. Reads Asylum Research Data Files (.ARDF).readARDF() reads image, note, and other data from the ARDF file into a Matlab

The retardation and surface effect can been removed if the thickness of sample is known.

With recent rapid advancement in electron microscopy instrumentation, in particular, bright electron sources and monochromators, valence electron energy-loss spectroscopy (VEELS) has become

Approximate the stray field gradient of a MFM probe using a magnetic dipole and simulated annealing to find the best parameters.

by local magnetic field gradients. Commun Phys 2, 145 (2019). https://doi.org/10.1038/s42005-019-0242-5[2] Corte-León, H., Volker, Neu, Manzin, Alessandra et al. Magnetic Force Microscopy: Comparison

Read Digital Micrograph files for electron microscopy

Computes the 2nd order orientation tensor diagonal from an optical or scanning electron micrograph

imrotate3_fast

version 1.1.0.0

by Dave

Fast 3D image rotations

(e.g. microscopy data), the speed differences are enormous, and allow for reduced memory demands.Note: imrotate3 performs a single rotation around an arbitrary axis (axis-angle), whereas imrotate3_fast

Atomic Force Microscopy Image Analysis

This is the software to analysis the atomic force microscopy images. Average feature size and area can be calculated using this software. Steps to follow - 1 - First remove any additional part of the

Calculates radially averaged 2D power spectrum for a surface roughness/topography

surface topography, which the topography is normally obtained by any 3D profilometry techniques, such as AFM (Atomic Force Microscopy), WLI (White Light Interferometry) and many other optical profilers. As

Script package for quantifying bacterial load within cells using images from Olympus IX81/Slidebook

This package includes a variety of scripts for analysis of microscopy images, using the SAFIRE screening platform. This package is useful for analyzing high-content screens of intracellular bacteria

Calculates radially averaged 2D power spectrum for a certain part of surface topography

topography is normally obtained by any 3D profilometry techniques, such as AFM (Atomic Force Microscopy), WLI (White Light Interferometry) and many other optical profilers.You need to provide 5 inputs to the

SAFIRE_CV1000

version 1.0.0.0

by Abigail Reens

Script package for quantifying bacterial load within cells using images from a CV1000 microscope

This package includes a variety of scripts for analysis of microscopy images, using the SAFIRE screening platform. This package is useful for analyzing high-content screens of intracellular bacteria

Automatic segmentation and morphological analysis of microvessels in histological tumour sections

, "An automatic algorithm for the segmentation and morphological analysis of microvessels in immunostained histological tumour sections", Journal of Microscopy, Volume 242, Issue 3, pages 262–278, June

An algorithm to generate clumped-sphere approximations of non-spherical particles

An algorithm to generate clumped-sphere approximation of non-spherical particles from particle STL files (X-ray micortomography, Selective Electron Microscopy etc), to be use in Discrete Element

Rapid fitting of Gaussian PSF models to a list of candidate positions in an image.

The quick and accurate localization of many emitters showing up as 2D Gaussian like shapes in an image is an important tool in fluorescence microscopy. Mostly this is used in the context of

Fast alignment and reconstruction algorithm for cryo-electron microscopy

cryo-electron microscopy images and the structure projections, greatly reducing the number of image transformations and comparisons that are computed. The files include an implementation of the SubspaceEM

StackSlider

version 1.1.0.0

by Otto Manneberg

GUI for displaying image stacks, e.g. time-resolved or z-stacked microscopy images.

Script package for quantifying bacterial load within cells using images from an ArrayScan microscope

This package includes a variety of scripts for analysis of microscopy images, using the SAFIRE screening platform. This package is useful for analyzing high-content screens of intracellular bacteria

View Image Stack GUI

version 1.0.0.0

by Tapan

Allows users to view a tiff stack (useful for time-lapse microscopy datasets)

drifty_shifty_deluxe.m

version 1.0.0.0

by Josh

Automatic spatial drift correction of images or video frames.

each image frame aligned. An instruction manual has been submitted to Microscopy Today and will hopefully be published in the near future.

Matlab2Gwyddion

version 1.1.0.0

by Jens Brauer

Save Matlab data from SPM/AFM scans for use with Gwyddion

What is Gwyddion?"Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for analysis of height fields obtained by scanning probe

Quantify relative localization of proteins based on STORM-based single molecule positional data

Super-resolution STochastic Optical Reconstruction Microscopy (STORM) achieves resolutions of 20 nm laterally and <50 nm in the z-dimension and yields 3D positions of individual molecules

Generate in 3D the diffusion gradient vector field as in Xu and Prince 1998

usage:[un vn wn] = dgvf_calc(I,sqrt(numel(I)), 0.5, 1, 1, 1, 1)Note: The code was developed with 3d flourescence microscopy images in mind (bright objects against dark background). Enforcement of boundary

Remove shading (or the un-even intensity background) of images

A common phenomenon in biomedical imaging is the presence of spurious intensity variations due to the sample of interest and the technique of acquisition. In light microscopy, the variation may

3D reconstruction algorithm for electron cryo-microscopy.

a Bayesian maximum-a-posteriori framework and uses an efficient optimization algorithm for the maximization. Evaluations using simulated and actual cryogenic electron microscopy data show resolution

Hyperspectral CARS microscopy and spectroscopy toolbox

Hyperspectral CARS microscopy and spectroscopy toolbox allows researchers easy analysis of their data.Toolbox focuses on image fusion, denoising and spectroscopy.

Segment the vessel branches from dynamic image of fluorescent microscopy

Segment the blood vessels from a dynamic image of fluorescent microscopy. == Install ======- Add all attached files to matlab path- Download "Better Skeletonization" from following URL and add to

WaveSurfer

version 1.0.0.0

by Adam

An application for acquiring neurophysiology data in Matlab

microscopy* Open source

Imports Gatan .DM3 format files with tags (images, spectra, & spectral images) into a MATLAB struct.

This script acts to import files from Gatan's .DM3 file format, utilized for electron microscopy, into a MATLAB structure. The fields of the MATLAB structure can then be referenced with the

3D volume visualization - with the light source always coming from the direction of the viewer

of the voxels along the X, Y and Z directions. In microscopy data, these are commonly different (so if the pixel size along X and Y are 100 nm and the Z axis spacing between sections is 1 micron, set

Converts a single image (microscopy, topogrpahy) into array of images.

Spectromicroscopic analysis of atmospheric nanoparticles (aerosols)

An automated data analysis method for atmospheric particles using scanning transmission X-ray microscopy coupled with near edge X-ray fine structure spectroscopy (STXM/NEXAFS). This method is applied

Perform color quantization based on user predefined color categories.

euclidean distance in the RGB color space. The user can also set a maximal color distance at which the pixels is considered unmatched. This program is used in image analysis for microscopy work.

3D image stack viewer

version 1.0.0.0

by boyexex

Current version only accept gray-scale images. Just format your image stack into a 3D array.

A good tool to display all kinds of 3D image stacksLSM (Laser scanning microscopy) imagesCT scan (x-ray) imagesMRI imagesConfocal microscopy imagesOCT (optical coherence tomography) images

Generate the point-spread function for a widefield fluorescence microscope

. of Asilomar Conference on Signals, Systems and Computers.[3] P. Pankajakshan (2009). Blind Deconvolution for Confocal Laser Scanning Microscopy. Ph.D. thesis, Universite de Nice Sophia-Antipolis.Author

STXM data analysis script collection with stack exploration GUI tool STACKLab

This is a MATLAB script collection developed at Lawrence Berkeley National Lab that can be used as a basis for Scanning Transmission X-ray Microscopy (STXM) data analysis. It includes routines for

Simple method to calculate the threshold of an image

fluorescence microscopy images in which most of the pixels are background and the background is approximately gaussian.There are a couple parameters than can be used to tune the threshold.

Multivariate Image Analysis of 4-dimensional image sequences using 2-step two-way and three-way ...

) sequences of images acquired at different depths using microscopy.Two approaches are included:1. 2-step two-way MIA using PCA, MCR. MAF and Simplisma. In this method, image sequences as a function of

HybridVel

version 1.1.0.0

by Pratik Chhatbar

Improved blood velocity measurements with a hybrid image filtering and iterative Radon transform

Red blood cells (RBCs) in plasma labeled with a fluorescent dye present as black disks on microscopy. Moving RBCs create black streaks on the space-time image, e.g., with line-scan imaging on

Creates color figure shadows - multiple shadows and multiple frames

Vivo Microscopy keywords: shadow box, figure shadow, multiple frames, multi frame view, volume data appearance, 2D/3D/N-D, tif/png/jpg, RGB, color

Read SPIDER files

version 1.1.0.0

by Bill Baxter

Read and write files in SPIDER format

SPIDER is a free image processing system for electron microscopy. It is used for three-dimensional reconstruction of single particle macromolecules, multivariate statistical classification, and

TACTICS Toolbox

version 1.3.0.0

by Raz Shimoni

TACTICS is an interactive platform for customized high content bioimaging analysis.

single-cell tracking and high-through output quantification of imaged cells. TACTICS include dedicated user interface and customized algorithms to analyse multiple time lapse microscopy experiments with a mouse

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