A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.

Batch_Filter_CaseStudy part 2

Bioimage Analyst

We will cover the theory behind some useful image preprocessing operations such as filtering for image restoration and feature enhancements, illumination compensation and background correction. We will then combine these operations and write a complete image analysis macro including image correction and 2D stitching of images coming from a large multiposition experiment.

Image Data Explorer


The Image Data Explorer is a Shiny app that allows the interactive visualization of images and ROIs associated with data points shown in a scatter plot. It is useful for exploring the relationships between images/ROIs and associated data represented in tabular format.

has function

EvaluateSegmentation Tool


A command line tool that allows to quantitatively compare two volumes of binary segmentations. Implements 22 different metrics for comparing segmentations such as Dice Coefficient, Hausdorff Distance and average Distance.