Microscopy Image Browser (MIB)

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

Microscopy Image Browser 2 (MIB2)

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

High-Throughput, Algorithmic Determination of Nanoparticle Structure from Electron Microscopy Images

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

Segmentation of WBC in microscopy images

Stain deconvolution followed by threshold based segmentation is used.

Synthetic Bright-Field Microscopy Image Generator

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

Filter noise and interpolate microscopy images in frequency domain

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

Nonlinear Drift Correction from Scanning Probe Microscopy (SPM) Orthogonal Image Pairs

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

AFM Image Analysis

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

Read .dm3 and .dm4 image files

Read Digital Micrograph files for electron microscopy

Open-Microscopy-Data-MATLAB

This is a tutorial demonstrating how to access open microscopy data and publish reusable and reproducible analyses in MATLAB

Analyse Open Microscopy Data in MATLAB^®A MATLAB Live Script with accompanyingJupyter^® Notebook,m fileandreproducible code capsule on Code Ocean^®to access and analyze Microscopy image data sets from

Segmentation of neurons in microscopy images

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

Imagic, MRC, DM and STAR file i/o

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

Image to Volume Conversion for Representing Materials Topography

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

Machine learning assisted hyperspectral imaging

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

Computationally Enhanced Quantitative Phase Microscopy

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

Transmittance limit for Digital Holographic Microscopy

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

Noise evaluation in transmission electron microscopy (TEM)

Scrips for evalutating the important noise parameters and correlations in TEM. Reconstruction of the point spread function from signal noise

microscopy.Sci Rep 15, 3815 (2025).https://doi.org/10.1038/s41598-025-85982-4So, if you use any of these scripts for your evaluations please cite the above paper.Please note, however, that the authors disclaim any

StackSlider

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

GUI for detection of cells for Integrated Light and Electron Microscopy

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

Stain Density Estimation

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

Measure Myelin-to-Axon Diameter

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

bids-matlab

MATLAB / Octave tools for BIDS datasets

Composites fibre orientation from one cross section

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

A Bayesian Adaptive Basis Algorithm for Single Particle Reconstruction

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

SubspaceEM: A Fast Maximum-a-posteriori Algorithm for Cryo-EM Single Particle Reconstruction

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

Vessel branch segmentation

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

Local_gradients

Particle localisation using local gradients

Local_gradientsThis package provides a set of tools for 3-D localisation of single particles in brightfield and fluorescent microscopy using local gradients.The package is provided in LabVIEW, Matlab

View Image Stack GUI

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

Automated Analysis of Platelet Aggregation in Microfluidics

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

Hyperspectral CARS Image Analysis

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.

SpineCounter

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

Optical Point Spread Function generator (with aberrations)

3D PSF of a microscopy objective starting Focal length, stop size and numerical aperture. Includes Aberrations, and illumination properties.

CellMAP

CellMAP: an open-source software tool to batch-process cell topography and elasticity maps collected by atomic force microscopy.

collected by atomic force microscopy ## DOI: https://doi.org/10.1186/s12859-025-06060-0## To cite this software: Allard, A., Liboz, M., Crépin, R. et al. CellMAP: an open-source software tool to batch-process

Interface detection in point cloud data (SRM & SMLM)

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 ©

Medical Imaging Toolbox Interface for Cellpose Library

Use Cellpose library in MATLAB

Segment cells from microscopy images using the Medical Imaging Toolbox™ Interface for Cellpose Library. The support package provides functionality for downloading pretrained models from the Cellpose

Reconstruct3D3wayFRET

3D-Reconstruction algorithm used for N-way FRET microscopy

neuropoly/axonseg

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.

Cell Shape Classifier

Time-lapse microscopy classification of 2D cells based on cell shape (Seiler et al., TERM, 2012)

Extract and display ROIs from a Zeiss CZI image

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

STXM Spectromicroscopy Particle Analysis Routines

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

drifty_shifty_deluxe.m

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.

coloc3D

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

Suite2P

Fast, complete two-photon pipeline

Best Infocus Image from Image Stack

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

Leica image format file loader

Read and preview of Leica's image format file.

Matlab2Gwyddion

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

Scalebar for images and plots

Scalebar for images and plots

example](src/examples/createImageExample.m) creates thefollowing pseudocoloured microscopy image and adds a 25 µm scale bar. From therepository root, run it with:```matlabaddpath("src/examples")createImageExample``` ### Plot dataThe

SimpleMScanner

Basic (demo) 2-photon microscope scanning software

STXM data analysis script collection - STACKLab

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

Control ZEN Blue and the microscope from MATLAB

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

ReadImageJROI

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

DM3 Import for Gatan Digital Micrograph

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

SAFIRE_ArrayScan

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

ARDF to Matlab

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

nd2read

Nikon ND2 File Reader

3D image stack viewer

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

Radially averaged surface roughness/topography power spectrum (PSD)

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

Read SPIDER files

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

Diffusion gradient vector field in 3D

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

imrotate3_fast

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