Artifacts using EBImage (16)

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Functions to visualize long vectors of integer data by means of Hilbert curves

Core package containing all the tools for simple and advanced source extraction. This is used to create inputs for 'ProFit', or for source detection, extraction and photometry in its own right.

Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analysing 3D point patterns.

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics.

FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.

flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This ...

Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing.

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

A problem when recording 3D fluorescent microscopy images is how to properly present these results in 2D. Maximum intensity projections are a popular method to determine the focal plane of each pixel in the image. The problem with this approach, however, is that out-of-focus elements will still be visible, making edges and fine structures difficult to detect. This package aims to resolve this problem by using the contrast around a given pixel to determine the focal plane, allowing for a much cleaner ...