Welcome to the Image Data Explorer Wiki!
Authors: Jean-Karim Heriche, Coralie Muller
In many bioimaging projects, image analysis produces quantitative descriptions of biological characteristics. These quantitative descriptions often take the form of numerical features associated with the images and regions of interest (ROIs, e.g. segmented objects) on those images. Examples of such features are mean intensity of a fluorescent marker and area it occupies. Plotting these features is often used to identify groups or outliers. However, it is sometimes difficult to associate abstract features to visual characteristics of the objects they describe. Typical questions that arise in this context are:
- are there features that can separate different groups?
- what do members of different groups look like?
- what do outliers look like?
To address such questions, it is desirable to simultaneously and interactively visualize data points and the corresponding images and ROIs. This motivated the development of the Image Data Explorer (IDE).
The main feature of the IDE consists in the linked visualization of images and data derived from these images presented in both a data table and a plot. Linking the three representations allows them to simultaneously reflect the user's selection of data points.
To help with data exploration, the IDE also offers methods for dimensionality reduction, clustering as well as classification and feature selection.
The IDE is a web-based app written in the R language using the shiny package.
- User manual:
- Developer manual:
- [App structure and conventions]
- [Adding new functionalities to a module]
- [Adding a new module]