Visualisation

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

Synonyms
Plotting
Description

Phindr3D is a comprehensive shallow-learning framework for automated quantitative phenotyping of three-dimensional (3D) high content screening image data using unsupervised data-driven voxel-based feature learning, which enables computationally facile classification, clustering and data visualization.

Please see our GitHub page and the original publication for details.

Viv

Description

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.

Rendering a pyramidal, multiplexed immunofluorescence OME-TIFF image of a human kidney using additive blending to render four image channels into a single RGB image in the client.
Description

KNIME workflow to visualize a dataset described by multiple quantitative features (ex: a list of samples or cells, each described with multiple morphological features) as a 3D cloud of points (each point corresponding to one sample/cell) as well as a line plot (1 line per sample/cell).

For the 3D plot, the workflow uses Principal Component Analysis (PCA) for dimensionality reduction, ie it simplifies the information for each sample from n-features to 3 pseudo-features which are used as x,y,z-coordinates for each sample. The original features should cover similar value range, to make sure the PCA is not biased towards the large values features. One option is to normalize the values (min/max or Z-score). 

Also make sure that the resulting PCA represents a decent % of the original data variance (at least 70%). Otherwise the PCA plot will not be representative of the original data-distribution. The % is shown in the title of the PCA plot.

The workflow is interactive and so selecting in one panel of the figure will highlight in the other panel too.

It was originally published for the visualization of phenotypic kidney features in zebrafish, but the workflow is generic by design and can be reused for any quantitative feature set. 

KNIME-Workflow
Description

MoBIE (Multimodal Big Image Data Exploration) is a framework for sharing and interactive browsing of multimodal big image data. The MoBIE Fiji viewer is based on BigDataViewer and enables browsing of MoBIE datasets. 

It is also called Platybrowser, and uses the n5 format.

Mobie
Description

The Morphonet Python API provide an easy interface to interact directly with the MorphoNet server. Very useful to upload, download your dataset and superimpose on it any quantitative and quantitative informations.