Imaging

Image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy. Tools included:

• 2D/3D single-particle tracking tool which can be used to track bright spots in 2D/3D movies over time.
• Optimal filament segmentation of 2D images. 
• Curvature filters for image filtering, denoising, and restoration. 
• Image naturalization for image enhancement based on gradient statistics of natural-scence images. 
• Tool for automatically send and distribute jobs on clusters and get back the results.
• Multi-region image segmentation of 2D and 3D images without needing to know the number of regions beforehand. 
• Squassh for globally optimal segmentation of piecewise constant regions in 2D and 3D images and for object-based co-localization analysis. 
• Tool for inferring spatial interactions between patterns of objects in images or between coordinates read from a file.
• Tool for robust, histogram-based background subtraction well suited to correct for inhomogeneous illumination artifacts.
• A tool to estimate the Point-Spread Function of the microscopy out of 2D fluorescence images.
• A tool to measure the 3D Point-Spread Function of a confocal microscope from an image stack.
• Addition of synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. 
• Convolution of an image with a Bessel function in order to simulate imaging with a microscope. 
• A utility to detect bright spots in images and estimate their center. 
• A utility to create manual segmentations to be used as ground truth to test and benchmark automatic segmentation algorithms.
• A tool for replacing one color in an image with another color.

This ImageJ plugin aligns the slices of a stack just like the stackreg plugin on which it is built. It allows to save the transformations and to apply them to another stack. It furthermore allows to register two stacks.

Quote:

The "Angiogenesis Analyzer" allows analysis of cellular networks. Typically, it can detect and analyze the pseudo vascular organization of endothelial cells cultured in gel medium

...a simple tool to quantify the ETFA (Endothelial Tube Formation Assay) experiment images by extracting characteristic information of the network.

The outputs are network feature parameters.

Sample images

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Pseudo-Phase-Contrast.tif.zip

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Fluo.tif.zip

Source code

https://imagej.nih.gov/ij/macros/toolsets/Angiogenesis%20Analyzer.txt

ITK-SNAP is a software application used to segment structures in 3D medical images. It can also be used as a 3D annotation tool for deep learning. It is based on ITK, VTK libraries.

Image segmentation based on the MOSAIC Discrete region competition algorithm.