Microscopy Image Browser (MIB)
Version 1.302.0.0Ilya Belevich
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)
Version 2.8020Ilya Belevich
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
Read .dm3 and .dm4 image files
Version 18.104.22.168Fred Sigworth
Read Digital Micrograph files for electron microscopy
Synthetic Bright-Field Microscopy Image Generator
Version 22.214.171.124Patrik Malm
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
High-Throughput, Algorithmic Determination of Nanoparticle Structure from Electron Microscopy Images
Version 126.96.36.199Chad Mirkin
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
Segmentation of WBC in microscopy images
Version 1.0.0Abhinav Gadge
Stain deconvolution followed by threshold based segmentation is used.
Nonlinear Drift Correction from Scanning Probe Microscopy (SPM) Orthogonal Image Pairs
Version 188.8.131.52Colin Ophus
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
Imagic, MRC, DM and STAR file i/o
Version 184.108.40.206Fred Sigworth
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
AFM Image Analysis
Version 220.127.116.11Prashant Patil
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
Version 18.104.22.168Otto Manneberg
GUI for displaying image stacks, e.g. time-resolved or z-stacked microscopy images.
Segmentation of neurons in microscopy images
Version 1.0.3Omer Yuval
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 cells for Integrated Light and Electron Microscopy
Version 22.214.171.124Jose Delpiano
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
Machine learning assisted hyperspectral imaging
Version 126.96.36.199Orly Liba
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
Image to Volume Conversion for Representing Materials Topography
Version 188.8.131.52Kateryna Artyushkova
Converts a single image (microscopy, topogrpahy) into array of images.
Stain Density Estimation
Version 1.0.2Abhishek Selokar
Stain Deconvolution is used to determine Stain density Estimation in H&E microscopy images
Measure Myelin-to-Axon Diameter
Version 184.108.40.206steed huang
The M-file is to calculate the g-ratio for Scanning or Transmission Electronic Microscopy.
Composites fibre orientation from one cross section
Version 220.127.116.11Matthew Bondy
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
Vessel branch segmentation
Version 18.104.22.168Hiroshi Kawaguchi
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
SubspaceEM: A Fast Maximum-a-posteriori Algorithm for Cryo-EM Single Particle Reconstruction
Version 22.214.171.124Nicha Dvornek
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
Leica image format file loader
Version 126.96.36.199Hiroshi Kawaguchi
Read and preview of Leica's image format file.
Version 188.8.131.52Dylan Muir
Read a TIFF stack as a memory-mapped tensor. Handles a large range of internal TIFF formats.
View Image Stack GUI
Allows users to view a tiff stack (useful for time-lapse microscopy datasets)
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.
Version 184.108.40.206Aldo 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 Image Analysis
Version 220.127.116.11Rajeev Yadav
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.
Version 18.104.22.168Dylan 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.
Version 2.0.0José Luis Ruiz
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
Extract and display ROIs from a Zeiss CZI image
Version 1.0.0Peter Nagy
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 ©
STXM Spectromicroscopy Particle Analysis Routines
Version 22.214.171.124Ryan Moffet
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
Version 126.96.36.199W. 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
Radially averaged surface roughness/topography power spectrum (PSD)
Version 188.8.131.52Mona Mahboob Kanafi
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
Version 184.108.40.206Jens 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
Best Infocus Image from Image Stack
Version 1.3Vikas Thapa
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 ZEN Blue and the microscope from MATLAB
Control the ZEN Blue microscope control software from within a MATLAB script
STXM data analysis script collection - STACKLab
Version 220.127.116.11Tobias Henn
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
DM3 Import for Gatan Digital Micrograph
Version 18.104.22.168Robert McLeod
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
Version 22.214.171.124Eftychios Pnevmatikakis
Complete Matlab pipeline for large scale calcium imaging data analysis
Version 126.96.36.199Eran Mukamel
Toolbox for automated sorting of cellular calcium signals from optical imaging data.
Version 1.3.1Ryoma Hattori
Image processing pipeline to correct motion artifacts and complex image distortions in neuronal calcium imaging data.
Version 1.0.0Katrin Deinhardt
Script to determine allowed baseline variability. Use together with script axon analysis.
Version 188.8.131.52Rob Campbell
Simple interactive tracing software for neuronal axons and dendrites
Version 184.108.40.206Jacob Bowen
DiffractIndex is a simple program for measuring diffraction ring diameters from TEM or XRD patterns
Version 220.127.116.11Abigail Reens
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
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
Novel Retinal Vessel Segmentation Algorithm: Fundus Images
Version 18.104.22.168Tyler Coye
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
Version 22.214.171.124Bill 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
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
Diffusion gradient vector field in 3D
Version 126.96.36.199Khaled Khairy
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.