149 results

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

Read Digital Micrograph files for electron microscopy

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

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

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

Stain deconvolution followed by threshold based segmentation is used.

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

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

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



by Otto Manneberg

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

Set up, train and apply a neural network for segmentation of neurons in microscopy images.

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

Estimates and plots the transmittance limit for a digital hologram in a 1-bit to 16-bit representation for the given setup parameters.

Retrieval of accurate phase maps from Digital Holographic Microscopy (DHM) is highly dependent on the representation of the carrier fringe pattern in the digital sensor. Physically, the contrast of

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

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

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

Stain Deconvolution is used to determine Stain density Estimation in H&E microscopy images

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

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

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

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

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

Read and preview of Leica's image format file.



by Dylan Muir

Read a TIFF stack as a memory-mapped tensor. Handles a large range of internal TIFF formats.

View Image Stack GUI


by Tapan

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



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.



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.

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.



by Dylan Muir

Read ROIs and ROI sets saved from ImageJ into MATLAB, without java.

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

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



by Marius Pachitariu

Fast, complete two-photon pipeline

Two programs that extract and display ROIs from Zeiss CZI images.

Code for detecting interfaces in super-resolution microscopy (SRM) data. Also works for other types of Poisson-distributed point cloud data.

SMLM_interface_detectionCode for detecting interfaces in super-resolution microscopy (SRM) data,typically single-molecule localization microscopy (SMLM).The code provided here is under Copyright ©



by Rob Campbell

Basic (demo) 2-photon microscope scanning software

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



by W. Bryan Smith

Finds, summarizes, and plots (if desired) 2-color colocalization from 3D images.

This script allows the user to load 3-D TIFF images, such as those derived from confocal or 2-photon microscopy, into the MATLAB workspace for analysis of colocalization between two images in 3-D

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



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

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

Control the ZEN Blue microscope control software from within a MATLAB script

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

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

Complete Matlab pipeline for large scale calcium imaging data analysis

Toolbox for automated sorting of cellular calcium signals from optical imaging data.

Recognize 3D structures in volumetric images


Version 1.3.1

by Ryoma Hattori

Image processing pipeline to correct motion artifacts and complex image distortions in neuronal calcium imaging data.

Script to determine allowed baseline variability. Use together with script axon analysis.

Simple interactive tracing software for neuronal axons and dendrites



by Jacob Bowen

DiffractIndex is a simple program for measuring diffraction ring diameters from TEM or XRD patterns


Version 1.0.0

by CY Y

Nikon ND2 File Reader

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

3D image stack viewer


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

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

Read SPIDER files


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



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

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

A comprehensive and interactive image analysis software tool for bacterial cell biology

A fast Tiff and BigTiff reader that provides acces to ScanImage-specific metadata.

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