Linux

Fiji plugin to segment oocyte and zona pellucida contours from transmitted light images and extract hundreds of morphological features to describe numerically the oocyte. Segmentation is based on trained neural networks (U-Net) that were trained on both mouse and human oocytes (in prophase and meiosis I) acquired in different conditions. They are freely avaialable on the github repository and can be retrained if necessary. Oocytor also have options to extract hundreds of morphological/intensity features to characterize manually the oocyte (eg perimeter, texture...). These features can also be used in machine learning pipeline for automatic phenotyping.

EPySeg is a package for segmenting 2D epithelial tissues. EPySeg also ships with a graphical user interface that allows for building, training and running deep learning models.

Training can be done with or without data augmentation (2D-xy and 3D-xyz data augmentation are supported). EPySeg relies on the segmentation_models library. EPySeg source code is available here. Cloud version available here.

VTK is an open-source software system for image processing, 3D graphics, volume rendering and visualization. VTK includes many advanced algorithms (e.g., surface reconstruction, implicit modeling, decimation) and rendering techniques (e.g., hardware-accelerated volume rendering, LOD control).

VTK is used by academicians for teaching and research; by government research institutions such as Los Alamos National Lab in the US or CINECA in Italy; and by many commercial firms who use VTK to build or extend products.

The origin of VTK is with the textbook "The Visualization Toolkit, an Object-Oriented Approach to 3D Graphics" originally published by Prentice Hall and now published by Kitware, Inc. (Third Edition ISBN 1-930934-07-6). VTK has grown (since its initial release in 1994) to a world-wide user base in the commercial, academic, and research communities.

The BioVoxxel Toolbox is a suite which contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis. The following plugins are hosted here:

• Extended Particle Analyzer
• Binary Feature Extractor
• Speckle Inspector
• Watershed Irregular Features
• EDM Binary Operations
• Filter Check
• Pseudo flat-field correction
• Convoluted Background Subtraction
• 2D Particle Distribution (Distribution_Analysis)
• Cluster Indicator
• SSIDC Cluster Indicator
• Gaussian weighted Median filter
• Adaptive Filter
• Enhance True Color Contrast
• Mode and Differential Limited Mean Binarization
• Basic Recursive Filter

Fast4DReg is a Fiji macro for drift correction for 2D and 3D video and is able to correct drift in all x-, y- and/or z-directions. Fast4DReg creates intensity projections along both axes and estimates their drift using cross-correlation based drift correction, and then translates the video frame by frame. Additionally, Fast4DReg can be used for alignment multi-channel 2D or 3D images which is particularly useful for instruments that suffer from a misalignment of channels.