Confocal fluorescence microscopy

ELEPHANT is a platform for 3D cell tracking, based on incremental and interactive deep learning.
It implements a client-server architecture. The server is built as a web application that serves deep learning-based algorithms. The client application is implemented by extending Mastodon, providing a user interface for annotation, proofreading and visualization.

FluoGAN is a fluorescence image deconvolution software combining the knowledge of acquisition physical model with gan. It takes a fluctuating sequence of blurred, undersampled and noisy images of the sample of interest  fixed sample as input from wide field or confocal and returns a super resolved image.

Junction Mapper is a semi-automated software (Java Desktop application) for analysing data from images of cells in close proximity to each other in monolayers. The focus of Junction Mapper is to measure the morphology of cell boundaries, define single junctions and quantify the length, area and intensity of the staining of different proteins localised at cell-cell contacts. The output are various unique parameters that assess the contacting interface between cells and up to two junctional markers.

Local Z Projector is an ImageJ2 plugin, available in Fiji, that can perform local-Z projection of a 3D stack, possibly over time, possibly very large.

LZP performs projection of a surface of interest on a 2D plane from a 3D image. It is a simple tool that focuses on usability and is designed to be adaptable to many different use cases and image quality.

• It can work with 3D movies over time with multiple channels.
• It can work with images much larger than available RAM out of the box.
• It takes advantage of computers with multiple cores, and can be used in scripts.

ND-SAFIR is a software for denoising n-dimentionnal images especially dedicated to microscopy image sequence analysis. It is able to deal with 2D, 3D, 2D+time, 3D+time images have one or more color channel. It is adapted to Gaussian and Poisson-Gaussian noise which are usually encountered in photonic imaging. Several papers describe the detail of the method used in ndsafir to recover noise free images (see references).

It is available either in Metamorph (commercial version), either as command line tool. Source are available on demand.

Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

Acquiarium is open source software (GPL) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation.

It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

The purpose of the workflow is ....

First you need

Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

MorphoGraphX is a free Linux application for the visualization and analysis of 3D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 3D live-imaged confocal data sets.

The main research interests adressed by MorphoGraphX are:

• Shape extraction
• Growth analysis
• Signal quantification
• Protein localization