Manual

VAST (Volume Annotation and Segmentation Tool) is a utility application for manual annotation of large EM stacks.

General labeling tool, used for a large variety of 3D data sets; electron-microscopic, multi-channel light-microscopic, and Micro-CT data sets as well as videos, and annotating arbitrary structures, regions and locations, depending on the user’s needs.

pyimagej provides a set of wrapper functions for integration between ImageJ and Python.

It also provides a high-level entry point for invoking ImageJ server APIs.

Collection of add-ons (recipes, scripts, demos,…) that will help you improve your day-to-day use of Amira-Avizo and PerGeos Software and make you gain both time and efficiency.
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Epina ImageLab is a Microsoft Windows-based multisensor imaging tool for processing and analyzing hyperspectral images. It is a modular system consisting of a basic engine, a graphical user interface, a chemometrics toolbox and optional user-supplied modules. It supports the most important spectroscopic imaging techniques, such as UV/Vis, infrared, Raman, THz, optical emission/absorption, and mass spectrometry. On top of that Epina ImageLab enables the user to merge hyperspectral images with maps of physical properties and conventional high-resolution color photos. 

Summary

napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (e.g. numpy, scipy). It includes critical viewer features out-of-the-box, such as support for large multi-dimensional data, and layering and annotation. By integrating closely with the Python ecosystem, napari can be easily coupled to leading machine learning and image analysis tools (e.g. scikit-image, scikit-learn, TensorFlow, PyTorch), enabling more user-friendly automated analysis.

Installation

• The installation procedure for Silicon Mac (M1 Processor, arm64 ) requires some tricks. As of Oct 2021, this procedure by Peter Sobolewski works but:
  • For installing pyqt5, use a slightly different command `brew install PyQt@5` to install PyQt5.