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)

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

Python Server for performing biomedical images analysis

Data Acquisition for Confocal Microscope and Spin Control Experiments

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. Manual image analysis is labor-intensive, time-consuming, and prone to human error. I compiled two notebooks to streamline two of the most commonly performed tasks in the analysis of confocal z-stack images: the generation of "pretty" maximum projections, and the analysis of pixel values/ fluorescence from sum projections.

3D Analysis of confocal images of microbial biofilms/communities

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

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

No description provided.

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.

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

[Pillow] Denoising Images retrieved from Confocal Calcium Imaging.

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

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.

Application to efficiently annotate dendritic spines from confocal microscopy images and analyze spine motility via automatic length calculation.

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.

A specialized image analysis tool for automated detection and analysis of dendritic spines in neuronal images. 2D Span Auto streamlines workflow for neuroscience researchers with intuitive modules for image processing, dendrite extraction, and morphological analysis. The software features multiple denoising and binarization methods, accurate spine