batch processing

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Pixel density-batch mode

Workflow Language: 
Icy Protocol
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LIF Projector

Workflow Language: 
ImageJ Macro Language
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Columbus Image Data Storage and Analysis System

Columbus is a combination of an image database (based on Omero, OME) and an image analysis engine based on Acapella (PerkinElmer). It is dedicated to cell culture based high content screening data and is used via a web interface.
It provides a set importers for automated microscopes such as Yokogawa CellVoyager, PerkinElmer Operetta, PerkinElmer Opera and data in Metamorph format.

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ilastik

ilastik (the image learning, analysis, and segmentation toolkit) provides non-experts with a menu of pre-built image analysis workflows. ilastik handles data of up to five dimensions (time, 3D space, and spectral dimension). Its workflows provide an interactive experience to give the user immediate feedback on the quality of the results yielded by her chosen parameters and/or labelings.

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Imaris

Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space.

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ilastik - Density Counting

Package/Library: 
ilastik
VIGRA

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