Janelia Workstation

• UpdatedMar 27, 2025
• Java

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

• UpdatedJan 3, 2022
• MATLAB

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

• UpdatedFeb 15, 2022
• ImageJ Macro

Python Server for performing biomedical images analysis

• UpdatedSep 27, 2023
• Python

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. …

• UpdatedMay 13, 2022
• Jupyter Notebook

3D Analysis of confocal images of microbial biofilms/communities

• UpdatedJun 5, 2024
• R

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

• UpdatedOct 17, 2022
• PHP

Data Acquisition for Confocal Microscope and Spin Control Experiments

• UpdatedJul 26, 2024
• Python

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

• UpdatedAug 7, 2024
• Python

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

• UpdatedOct 10, 2018
• Java

Analysis performed for the Belyaeva et.al PNAS 2017 Paper

• UpdatedJul 18, 2020
• R

• UpdatedJul 8, 2022
• MATLAB

Képalkotás szenzor adatokból

• UpdatedFeb 5, 2024

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

• UpdatedMay 26, 2020
• R

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

• UpdatedOct 15, 2022
• Python

[Pillow] Denoising Images retrieved from Confocal Calcium Imaging.

• UpdatedApr 3, 2024
• Python

Versatile Fiji-imagej macro for 2D quantification of each marker inside your immunofluorescence staining in less of 1 minute per image. Control critical steps for segmentation.

• UpdatedNov 2, 2023
• ImageJ Macro

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.

• UpdatedNov 29, 2024
• Python

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

• UpdatedMay 25, 2020
• R

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

• UpdatedSep 7, 2022
• R