Janelia Workstation

Simulation for sensorless adaptive optics (Confocal microscopy, Modal method)

ImageJ / Fiji macro to automatically export Leica LIF file as individual images (batch mode available)

Imaging experiments in Biology often involve the acquisition of confocal z-stack images to quantify fluorescent signal in a biological sample. These z-stacks are usually analyzed using open-source programs such as FIJI, which are notoriously frustrating to work with, and do not facility intuitive high-throughput analysis of many images at once. …

Python Server for performing biomedical images analysis

3D Analysis of confocal images of microbial biofilms/communities

🧪 Reproducing the concept of Confocal Laser Scanning Microscope. Using Arduino and easily found materials. Generating images in Grayscale just for fun.

Data Acquisition for Confocal Microscope and Spin Control Experiments

A tool to accurately normalize and visualize protein distribution in 3D structures imaged with confocal microscopy using z-stacks.

Képalkotás szenzor adatokból

Analysis performed for the Belyaeva et.al PNAS 2017 Paper

Automated determination of cell membrane curvature from 3D stacks using the radius of osculating circle approach.

Blob Inspector is a software designed to analyze blobs in biological images. It provides several common tools for computing metrics related to the blobs, such as coordinates, size, density, and distances.

Quantification of actin dynamics using difference maps (Vidali et al, 2010, The Plant Cell)

Analysis of actin dynamics using the method described by Higaki et al. (2009).

[Pillow] Denoising Images retrieved from Confocal Calcium Imaging.

3D surface reconstruction from confocal microscopy stacks. This software package has been created for the anaylis of 3D vesicle shapes.

Repository containing methods applied for the analysis of the data in the SERCA publication

The MatLab code takes confocal TIFF images of cells as input and plots the distribution of different channels after segmentation of the image into features bases on the type of organelles. For getting the membrane features, distance transform is used to obtain a continuos membrane region.