Re-occurs among biii.info tags (visualisation, rendering, viewer, classification, ...)

Synonyms
Plotting

DragonFly

Description

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.

DragonFly

Neuroglancer

Description

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

 

Neuroglancer

FPBioimage

Description

FPBioimage is a volumetric visualization tool which runs in all modern web browsers. Try the tool yourself at our example site here.

has function

PYME

Description

The PYthon Microscopy Environment is an open-source package providing image acquisition and data analysis functionality for a number of microscopy applications, but with a particular emphasis on single molecule localisation microscopy (PALM/STORM/PAINT etc ...). The package is multi platform, running on Windows, Linux, and OSX.

It comes with 3 main modules:

  • PYMEAcquire - Instrument control and simulation
  • dh5view - Image Data Analysis and Viewing
  • VisGUI - Visualising Localization Data Sets

Visualization of 3D images with Matlab

Bioimage Analyst
Developer

In this session we will use a 3D multichannel reconstruction of zebrafish larva to explore the visualization capabilities of Matlab. We will start from extracting and inspecting single slices and will continue with combining multiple channels, finally generating a surface rendering for visual colocalization analysis.During the process we will review methods for manipulating multidimensional arrays, including resizing, reshaping and conditional selection.

Tumor Blood Vessels: 3D Tubular Network Analysis

Bioimage Analyst
Developer

In this session, we will implement a simple ImageJ macro to segment and analyze the blood vessel network of a subcutaneous tumor. The analysis is fully performed in 3D, and possible strategies to extract statistics of the network geometry and interactively visualize the results are also discussed and implemented.

CellProfiler Analyst CPA

Description

CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CPA provides tools for exploring and analyzing multidimensional data, particularly data from high-throughput, image-based experiments analyzed by its companion image analysis software, CellProfiler.

CPA