Slice rendering

Relate is a correlative software package optimised to work with EM, EDS, EBSD, & AFM data and images.  It provides the tools you need to correlate data from different microscopes, visualise multi-layered data in 2D and 3D, and conduct correlative analyses.

• Combining data from different imaging modalities (e.g. AFM, EDS & EBSD)

• Interactive display of multi-layer correlated data

• Analytical tools for metadata interrogation

• Documented workflows and processes

Correlate

• Import data from AZtec using the H5oina file format
• Import AFM data
• Correlate both sets of data using intuitive image overlays and image matching tools
• Produce combined multimodal datasets

Visualise

• 2D display of multi-layered data
• 3D visualisation of topography combined with AFM material properties, EM images, and EDS & EBSD map overlays
• Customisation of colour palettes, data overlays, image rendering options, and document display
• Export images and animations

Analyse

• Generate profile (cross section) views of multimodal data
• Measure and quantify data across multiple layers
• Analyse areas via data thresholding using amount of x-ray counts, phase maps, height, or other material properties.
• Select an extensive range of measurement parameters
• Export analytical data to text or CSV files

webKnossos is an open-source data sharing and annotation platform for tera-scale 2D and 3D image datasets.

The core features of webKnossos are:

• fast 3D data streaming
• share links to specific locations in the data
• uniquely fast skeleton annotation (flight mode) and
• efficient volume annotation
• mesh rendering
• collaboration and sharing tools

webKnossos facilitates image analysis workflows on multi-terabyte datasets, including visualization of raw and multi-modal microscopy data, distributed training data generation and proof-reading of automatic segmentation.

As a scientific resource, webknossos.org serves as a database for published image datasets including their annotations.

Viv is a JavaScript library providing utilities for rendering primary imaging data. Viv supports WebGL-based multi-channel rendering of both pyramidal and non-pyramidal images. The rendering components of Viv are provided as Deck.gl layers, facilitating image composition with existing layers and updating rendering properties within a reactive paradigm.

Paintera is a general visualization tool for 3D volumetric data and proof-reading in segmentation/reconstruction with a primary focus on neuron reconstruction from electron micrographs in connectomics. It features/supports:

•  Views of orthogonal 2D cross-sections of the data at arbitrary angles and zoom levels
•  Mipmaps for efficient display of arbitrarily large data at arbitrary scale levels
•  Label data
  •  Painting
  •  Manual agglomeration
  •  3D visualization as polygon meshes
    •  Meshes for each mipmap level
    •  Mesh generation on-the-fly via marching cubes to incorporate painted labels and agglomerations in 3D visualization. Marching Cubes is parallelized over small blocks. Only relevant blocks are considered (huge speed-up for sparse label data).

Paintera is implemented in Java and makes extensive use of the UI framework JavaFX