Image visualisation

MorphoNet is a novel concept of web-based morphodynamic browser to visualise and interact with complex datasets, with applications in research and teaching. 

MorphoNet offers a comprehensive palette of interactions to explore the structure, dynamics and variability of biological shapes and its connection to genetic expressions. 

By handling a broad range of natural or simulated morphological data, it fills a gap which has until now limited the quantitative understanding of morphodynamics and its genetic underpinnings by contributing to the creation of ever-growing morphological atlases.

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.  

Dragonfly is a software platform for the intuitive inspection of multi-scale multi-modality image data. Its user-friendly experience translates into powerful quantitative findings with high-impact visuals, driven by nuanced easy-to-learn controls.

For segmentation: It provides an engine fior machine Learning, Watershed and superpixel methods, support histological data .

It offers a 3D viewer, and python scripting capacities .

It is free for reserach use, but not for commercial usage.

Web based viewer developped for google for very big data: 

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). The segmentation has to be done before loading the dataset, it is not done Inside the viewer.

This is not an official Google product.

It has among other the nice feature of beeing able to generate url for sharing a specific view.

Note that the only supported browser for now are 

• Chrome >= 51
• Firefox >= 46