FPBioimage

Description

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

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Image Data Explorer

Description

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.

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EvaluateSegmentation Tool

Description

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. 

Automated workflow for parallel Multiview Reconstruction

Description

Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation. 

VascuSynth

Description

VascuSynth is an ITK-based synthetic image generator. It synthesizes volumetric images of vascular trees and generates a .gxl file of the ground-truth tree structure. VascuSynth receives a number of .txt configuration files and is capable of generating both ground truth ('ideal') images and images with added noise. The user is capable of choosing from a set simple noise additions and artefacts.

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Nuclei Tracking (ImageJ)

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3D Fill holes (mcib3d)

Description

Runs fill holes operation on 3D images.

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Maximum (3D) VIB Protocol

Description

This component convolves the image with maximum filter. Each voxel is set to the maximum value of its neighborhood. The neighborhood is defined by a kernel, which has a diameter of 3 voxels.

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ROI Measure

Description

ROI measurement plug-in for Icy.

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