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

Stain deconvolution followed by threshold based segmentation is used.

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

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

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

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 ©

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

Toolbox for Quantitative Image Analysis

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

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

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

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

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

This code can make an in focus image from multiple images that have been taken at different focuses.

This code can make an in focus image from multiple images that have been taken at different focuses.Optimal for optical microscopy where there is a slant or too high surface roughness.Currently

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

Toolbox for 4D-STEM data processing enabling the creation of a single 2D powder diffraction image and its 1D radial average.

, E.; Krzyzanek, V. High Resolution Powder Electron Diffraction in Scanning Electron Microscopy. Materials 2021, 14, 7550. https://doi.org/10.3390/ma14247550

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

Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3

deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy Weisong Zhao1,3, Shiqun Zhao 2,3, Liuju Li 2,3,Haoyu Li1,✉Liangyi Chen2,✉1 School of Instrumentation Science and

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.

Visualization and quantification of spatiotemporal membrane signaling

This MATLAB package is used to extract, visualize, and quantify spatiotemporal membrane signaling of time resolved 3D confocal microscopy observed single cells. It provides - basic cell parameter

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

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

快速随机读写5D图像格式，目前支持读入 Olympus OIR 和读写 OME-TIFF，比市面上流行的竞品BioFormats要快得多。

OIR这是Olympus显微镜默认的输出格式，为无限加尾优化。文件为无索引的多块结构，由块头标识其类型为元数据或像素值。因文件内无索引，为了实现快速随机读入，首次启动需要建立索引，并在同目录下保存索引文件，需要一定时间。以后再次打开就比较快了。本格式为Olympus私有格式，未公开详细文件规范，因此仅支持读入，不支持写出。C++核心：OirReaderMexMATLAB接口类：Image5D.OirReader，可在MATLAB中用doc Image5D.OirReader命令查看详细文档，以下简要列出接口：classdef OirReader4㎇文件的问题。BigTiff是TIFF格式的变体，解决了4㎇限制的问题。TIFF和BigTiff格式规范OME-TIFF但是，很多时候，高、宽、IFD，这3个维度并不足以满足我们的需求，于是出现了OME（Open 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

本工具箱可以像访问MATLAB数组一样高速读写OME-TIFF文件。仅支持Windows操作系统。

Format，标签图像文件格式）是一种广泛使用的多图像存档文件格式，可以存储多张2D图像，每个像素也可以是1、2或4字节（称位深度或SizeP），它们线性排列在被称为IFD的维度（称I维度）上，每个IFD类似于视频的一“帧”，除了像素数值以外还包含高度（Y维度）、宽度（X维度）等元数据信息，每一项元数据被称为一个标签。TIFF规范规定了每个IFD都必须包含的，所谓必需标签，以及一些可选包含的标签。经典的TIFF格式存在无法处理>4㎇文件的问题。BigTiff是TIFF格式的变体，解决了4㎇限制的问题。TIFF和BigTiff格式规范详见：https://www.awaresystems.be/imaging/tiff.htmlOME-TIFF但是，很多时候，高、宽、IFD，这3个维度并不足以满足我们的需求，于是出现了OME（Open Microscopy Environment，开放显微镜环境）-TIFF扩展格式，将I维度扩展为C, Z

This code performs the image processing required to convert a series of micrographs of a cantilever-free probe into a topographic map.

microscopy. Nat. Commun. 2021, 12 (1), 393.https://doi.org/10.1038/s41467-020-20612-3If used in a publication, please cite this reference for proper attribution

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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.

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

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

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

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

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

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 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

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.

An application for acquiring neurophysiology data in Matlab

microscopy* Open source