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OMERO.webtagging is the umbrella name for tools developed to enhance use of text annotations (tags) in OMERO. There are two tools at present, autotag and tagsearch.

Align aligns images relative to each other, for example, to correct shifts in the optical path of a microscope in each channel of a multi-channel set of images.

## Introduction CellCognition is a computational framework dedicated to the automatic analysis of live cell imaging data in the context of High-Content Screening (HCS). It contains algorithms for segmentation of cells and cellular compartments based on various fluorescent markers, features to describe cellular morphology by both texture and shape, tools for visualizing and annotating the phenotypes, classification, tracking and error correction. Events such as mitosis can be automatically identified and aligned to study the temporal kinetics of various cellular processes during cell cycle.

WIS-PhagoTracker is a software application for quantitative analysis of high throughput cell migration assay. The cell migration assay is based on a modified Phagokinetic tracks procedure, in which motile cells "leave their tracks" on a specialized surface. These tracks are visualized using a screening microscope.

WIS-PhagoTracker enables morphometric analysis of such tracks. It uses multiscale segmentation algorithm for fine detection of tracks and cells boundaries.

VIGRA is a free C++ and Python library that provides fundamental image processing and analysis algorithms. Its generic architecture allows it to be used in many different application contexts and ecosystems. It is designed as an intelligent library (using the C++ template mechanism) which allows users to write code at a fairly high level of abstraction and optimizes away the abstraction overhead upon compilation.

WIS-NeuroMath - is a software tool for automated analysis and quantification of fluorescent microscopy images of Nerve cells, in both in vivo and in vitro preparations. It allows for accurate detection of neurites in challenging images. Following neurite detection, different types of processing can be carried: Cell Morphology of cultured neurons, Neurite Length Analysis and Ganglion Explant Analysis. Usefull also for angiogenesis analysis.

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This plugin allows to apply a free affine transformation to a 2D image in an interactive way.

This plugin threshold an image using the Maximum Entropy algorithm, which aims at maximizing the inter-class entropy. Entropy is defined as -sum(p.*log2(p)), where p contains the histogram bin counts. This thresholding is very useful to segment images with few bright objects on large dark background. In ImageJ/FIJI you can acces this tool in Image->Adjust->Threshold and choose in the list In Aphelion, you can access this tool in Seglmentation->Threshold-> AphImgEntropyThreshold

EnhanceEdges enhances or identifies edges in an image, which can improve object identification or other downstream image processing.

This plugin allows to open images embedded in PDFs.